Tutorial for Mesoscale Two-Photon Calcium Imaging of Population Level Odor Responses from the Mouse Olfactory Bulb.¶
This tutorial shows how to access the data related to DANDI:001170 using pynwb.
This dataset contains the 2-photon calcium imaging, treadmill position and velocity traces and odor stimulus events, along with subject and session metadata.
Contents:
Select the subject and session you want to load¶
subject_id = 134
session_id = 22
nwbfile_path = f"sub-{subject_id}/sub-{subject_id}_ses-{session_id}_behavior+ophys.nwb"
Streaming an NWB file ¶
This section demonstrates how to access the files on the DANDI Archive without downloading them. Based on the Streaming NWB files tutorial from PyNWB.
The dandi.dandiapi.DandiAPIClient can be used to get the S3 URL of the NWB file stored in the DANDI Archive.
from dandi.dandiapi import DandiAPIClient
dandiset_id = "001170"
with DandiAPIClient() as client:
asset = client.get_dandiset(dandiset_id, 'draft').get_asset_by_path(nwbfile_path)
s3_url = asset.get_content_url(follow_redirects=1, strip_query=False)
We will use remfile for streaming the file. You can read more about remfile at this tutorial section.
import h5py
import remfile
file = remfile.File(s3_url)
h5_file = h5py.File(file, "r")
Reading an NWB file ¶
This section demonstrates how to read an NWB file using pynwb.
Based on the NWB File Basics tutorial from PyNWB.
An NWBFile represents a single session of an experiment. Each NWBFile must have a session description, identifier, and session start time.
Reading is carried out using the NWBHDF5IO class. To read the NWB file use the read mode ("r") to retrieve an NWBFile object.
from pynwb import NWBHDF5IO
io = NWBHDF5IO(file=h5_file, load_namespaces=True)
nwbfile = io.read()
nwbfile
root (NWBFile)
session_start_time
2022-07-21 00:00:00-05:00timestamps_reference_time
2022-07-21 00:00:00-05:00file_create_date
0
2024-08-07 00:21:45.469158+02:00experimenter
('Pirhayatifard, Delaram', 'Hanson, Elizabeth', 'Pfaffinger, Paul', 'Arenkiel, Benjamin', 'Reimer, Jacob')related_publications
('https://doi.org/10.1101/2023.04.24.538157', 'https://icml-compbio.github.io/2023/papers/WCBICML2023_paper122.pdf')acquisition
treadmill_position
data
timestamps
timestamp_link
two_photon_series_FOV1_channel1
data
timestamps
dimension
imaging_plane
optical_channel
0
device
two_photon_series_FOV2_channel1
data
timestamps
dimension
imaging_plane
optical_channel
0
device
two_photon_series_FOV3_channel1
data
timestamps
dimension
imaging_plane
optical_channel
0
device
keywords
processing
behavior
data_interfaces
treadmill_velocity
data
timestamps (link to acquisition/treadmill_position/timestamps)
ophys
data_interfaces
average_images
images
average_image_FOV1_channel1
average_image_FOV2_channel1
average_image_FOV3_channel1
correlation_images
images
correlation_image_FOV1_channel1
correlation_image_FOV2_channel1
correlation_image_FOV3_channel1
fluorescence
roi_response_series
fluorescence_FOV1_channel1
data
timestamps
rois
table
imaging_plane
optical_channel
0
device
table
| pixel_mask | |
|---|---|
| id | |
| 0 | [[150, 83, 1.0], [151, 83, 1.0], [152, 83, 1.0], [153, 83, 1.0], [154, 83, 1.0], [155, 83, 1.0], [156, 83, 1.0], [157, 83, 1.0], [158, 83, 1.0], [159, 83, 1.0], [160, 83, 1.0], [161, 83, 1.0], [149, 84, 1.0], [150, 84, 1.0], [151, 84, 1.0], [152, 84, 1.0], [153, 84, 1.0], [154, 84, 1.0], [155, 84, 1.0], [156, 84, 1.0], [157, 84, 1.0], [158, 84, 1.0], [159, 84, 1.0], [160, 84, 1.0], [161, 84, 1.0], [162, 84, 1.0], [163, 84, 1.0], [147, 85, 1.0], [148, 85, 1.0], [149, 85, 1.0], [150, 85, 1.0], [151, 85, 1.0], [152, 85, 1.0], [153, 85, 1.0], [154, 85, 1.0], [155, 85, 1.0], [156, 85, 1.0], [157, 85, 1.0], [158, 85, 1.0], [159, 85, 1.0], [160, 85, 1.0], [161, 85, 1.0], [162, 85, 1.0], [163, 85, 1.0], [164, 85, 1.0], [147, 86, 1.0], [148, 86, 1.0], [149, 86, 1.0], [150, 86, 1.0], [151, 86, 1.0], [152, 86, 1.0], [153, 86, 1.0], [154, 86, 1.0], [155, 86, 1.0], [156, 86, 1.0], [157, 86, 1.0], [158, 86, 1.0], [159, 86, 1.0], [160, 86, 1.0], [161, 86, 1.0], [162, 86, 1.0], [163, 86, 1.0], [164, 86, 1.0], [146, 87, 1.0], [147, 87, 1.0], [148, 87, 1.0], [149, 87, 1.0], [150, 87, 1.0], [151, 87, 1.0], [152, 87, 1.0], [153, 87, 1.0], [154, 87, 1.0], [155, 87, 1.0], [156, 87, 1.0], [157, 87, 1.0], [158, 87, 1.0], [159, 87, 1.0], [160, 87, 1.0], [161, 87, 1.0], [162, 87, 1.0], [163, 87, 1.0], [164, 87, 1.0], [147, 88, 1.0], [148, 88, 1.0], [149, 88, 1.0], [150, 88, 1.0], [151, 88, 1.0], [152, 88, 1.0], [153, 88, 1.0], [154, 88, 1.0], [155, 88, 1.0], [156, 88, 1.0], [157, 88, 1.0], [158, 88, 1.0], [159, 88, 1.0], [160, 88, 1.0], [161, 88, 1.0], [162, 88, 1.0], [163, 88, 1.0], [148, 89, 1.0], ...] |
| 1 | [[152, 91, 1.0], [153, 91, 1.0], [154, 91, 1.0], [155, 91, 1.0], [156, 91, 1.0], [150, 92, 1.0], [151, 92, 1.0], [152, 92, 1.0], [153, 92, 1.0], [154, 92, 1.0], [155, 92, 1.0], [156, 92, 1.0], [157, 92, 1.0], [149, 93, 1.0], [150, 93, 1.0], [151, 93, 1.0], [152, 93, 1.0], [153, 93, 1.0], [154, 93, 1.0], [155, 93, 1.0], [156, 93, 1.0], [157, 93, 1.0], [158, 93, 1.0], [148, 94, 1.0], [149, 94, 1.0], [150, 94, 1.0], [151, 94, 1.0], [152, 94, 1.0], [153, 94, 1.0], [154, 94, 1.0], [155, 94, 1.0], [156, 94, 1.0], [157, 94, 1.0], [158, 94, 1.0], [159, 94, 1.0], [148, 95, 1.0], [149, 95, 1.0], [150, 95, 1.0], [151, 95, 1.0], [152, 95, 1.0], [153, 95, 1.0], [154, 95, 1.0], [155, 95, 1.0], [156, 95, 1.0], [157, 95, 1.0], [158, 95, 1.0], [159, 95, 1.0], [160, 95, 1.0], [148, 96, 1.0], [149, 96, 1.0], [150, 96, 1.0], [151, 96, 1.0], [152, 96, 1.0], [153, 96, 1.0], [154, 96, 1.0], [155, 96, 1.0], [156, 96, 1.0], [157, 96, 1.0], [158, 96, 1.0], [159, 96, 1.0], [160, 96, 1.0], [147, 97, 1.0], [148, 97, 1.0], [149, 97, 1.0], [150, 97, 1.0], [151, 97, 1.0], [152, 97, 1.0], [153, 97, 1.0], [154, 97, 1.0], [155, 97, 1.0], [156, 97, 1.0], [157, 97, 1.0], [158, 97, 1.0], [159, 97, 1.0], [160, 97, 1.0], [161, 97, 1.0], [147, 98, 1.0], [148, 98, 1.0], [149, 98, 1.0], [150, 98, 1.0], [151, 98, 1.0], [152, 98, 1.0], [153, 98, 1.0], [154, 98, 1.0], [155, 98, 1.0], [156, 98, 1.0], [157, 98, 1.0], [158, 98, 1.0], [159, 98, 1.0], [160, 98, 1.0], [161, 98, 1.0], [148, 99, 1.0], [149, 99, 1.0], [150, 99, 1.0], [151, 99, 1.0], [152, 99, 1.0], [153, 99, 1.0], [154, 99, 1.0], [155, 99, 1.0], [156, 99, 1.0], ...] |
| 2 | [[145, 100, 1.0], [146, 100, 1.0], [147, 100, 1.0], [143, 101, 1.0], [144, 101, 1.0], [145, 101, 1.0], [146, 101, 1.0], [147, 101, 1.0], [148, 101, 1.0], [149, 101, 1.0], [142, 102, 1.0], [143, 102, 1.0], [144, 102, 1.0], [145, 102, 1.0], [146, 102, 1.0], [147, 102, 1.0], [148, 102, 1.0], [149, 102, 1.0], [150, 102, 1.0], [141, 103, 1.0], [142, 103, 1.0], [143, 103, 1.0], [144, 103, 1.0], [145, 103, 1.0], [146, 103, 1.0], [147, 103, 1.0], [148, 103, 1.0], [149, 103, 1.0], [150, 103, 1.0], [151, 103, 1.0], [140, 104, 1.0], [141, 104, 1.0], [142, 104, 1.0], [143, 104, 1.0], [144, 104, 1.0], [145, 104, 1.0], [146, 104, 1.0], [147, 104, 1.0], [148, 104, 1.0], [149, 104, 1.0], [150, 104, 1.0], [151, 104, 1.0], [152, 104, 1.0], [140, 105, 1.0], [141, 105, 1.0], [142, 105, 1.0], [143, 105, 1.0], [144, 105, 1.0], [145, 105, 1.0], [146, 105, 1.0], [147, 105, 1.0], [148, 105, 1.0], [149, 105, 1.0], [150, 105, 1.0], [151, 105, 1.0], [152, 105, 1.0], [139, 106, 1.0], [140, 106, 1.0], [141, 106, 1.0], [142, 106, 1.0], [143, 106, 1.0], [144, 106, 1.0], [145, 106, 1.0], [146, 106, 1.0], [147, 106, 1.0], [148, 106, 1.0], [149, 106, 1.0], [150, 106, 1.0], [151, 106, 1.0], [152, 106, 1.0], [139, 107, 1.0], [140, 107, 1.0], [141, 107, 1.0], [142, 107, 1.0], [143, 107, 1.0], [144, 107, 1.0], [145, 107, 1.0], [146, 107, 1.0], [147, 107, 1.0], [148, 107, 1.0], [149, 107, 1.0], [150, 107, 1.0], [151, 107, 1.0], [152, 107, 1.0], [139, 108, 1.0], [140, 108, 1.0], [141, 108, 1.0], [142, 108, 1.0], [143, 108, 1.0], [144, 108, 1.0], [145, 108, 1.0], [146, 108, 1.0], [147, 108, 1.0], [148, 108, 1.0], [149, 108, 1.0], [150, 108, 1.0], [151, 108, 1.0], [152, 108, 1.0], [140, 109, 1.0], [141, 109, 1.0], ...] |
| 3 | [[138, 90, 1.0], [139, 90, 1.0], [140, 90, 1.0], [137, 91, 1.0], [138, 91, 1.0], [139, 91, 1.0], [140, 91, 1.0], [141, 91, 1.0], [136, 92, 1.0], [137, 92, 1.0], [138, 92, 1.0], [139, 92, 1.0], [140, 92, 1.0], [141, 92, 1.0], [142, 92, 1.0], [143, 92, 1.0], [135, 93, 1.0], [136, 93, 1.0], [137, 93, 1.0], [138, 93, 1.0], [139, 93, 1.0], [140, 93, 1.0], [141, 93, 1.0], [142, 93, 1.0], [143, 93, 1.0], [144, 93, 1.0], [134, 94, 1.0], [135, 94, 1.0], [136, 94, 1.0], [137, 94, 1.0], [138, 94, 1.0], [139, 94, 1.0], [140, 94, 1.0], [141, 94, 1.0], [142, 94, 1.0], [143, 94, 1.0], [144, 94, 1.0], [134, 95, 1.0], [135, 95, 1.0], [136, 95, 1.0], [137, 95, 1.0], [138, 95, 1.0], [139, 95, 1.0], [140, 95, 1.0], [141, 95, 1.0], [142, 95, 1.0], [143, 95, 1.0], [144, 95, 1.0], [145, 95, 1.0], [134, 96, 1.0], [135, 96, 1.0], [136, 96, 1.0], [137, 96, 1.0], [138, 96, 1.0], [139, 96, 1.0], [140, 96, 1.0], [141, 96, 1.0], [142, 96, 1.0], [143, 96, 1.0], [144, 96, 1.0], [135, 97, 1.0], [136, 97, 1.0], [137, 97, 1.0], [138, 97, 1.0], [139, 97, 1.0], [140, 97, 1.0], [141, 97, 1.0], [142, 97, 1.0], [143, 97, 1.0], [144, 97, 1.0], [135, 98, 1.0], [136, 98, 1.0], [137, 98, 1.0], [138, 98, 1.0], [139, 98, 1.0], [140, 98, 1.0], [141, 98, 1.0], [142, 98, 1.0], [143, 98, 1.0], [144, 98, 1.0], [136, 99, 1.0], [137, 99, 1.0], [138, 99, 1.0], [139, 99, 1.0], [140, 99, 1.0], [141, 99, 1.0], [142, 99, 1.0], [143, 99, 1.0], [137, 100, 1.0], [138, 100, 1.0], [139, 100, 1.0], [140, 100, 1.0], [141, 100, 1.0], [142, 100, 1.0], [138, 101, 1.0], [139, 101, 1.0], [140, 101, 1.0]] |
... and 13 more rows.
fluorescence_FOV2_channel1
data
timestamps
rois
table
imaging_plane
optical_channel
0
device
table
| pixel_mask | |
|---|---|
| id | |
| 0 | [[159, 51, 1.0], [160, 51, 1.0], [154, 52, 1.0], [155, 52, 1.0], [156, 52, 1.0], [157, 52, 1.0], [158, 52, 1.0], [159, 52, 1.0], [160, 52, 1.0], [161, 52, 1.0], [162, 52, 1.0], [151, 53, 1.0], [152, 53, 1.0], [153, 53, 1.0], [154, 53, 1.0], [155, 53, 1.0], [156, 53, 1.0], [157, 53, 1.0], [158, 53, 1.0], [159, 53, 1.0], [160, 53, 1.0], [161, 53, 1.0], [162, 53, 1.0], [163, 53, 1.0], [150, 54, 1.0], [151, 54, 1.0], [152, 54, 1.0], [153, 54, 1.0], [154, 54, 1.0], [155, 54, 1.0], [156, 54, 1.0], [157, 54, 1.0], [158, 54, 1.0], [159, 54, 1.0], [160, 54, 1.0], [161, 54, 1.0], [162, 54, 1.0], [163, 54, 1.0], [149, 55, 1.0], [150, 55, 1.0], [151, 55, 1.0], [152, 55, 1.0], [153, 55, 1.0], [154, 55, 1.0], [155, 55, 1.0], [156, 55, 1.0], [157, 55, 1.0], [158, 55, 1.0], [159, 55, 1.0], [160, 55, 1.0], [161, 55, 1.0], [162, 55, 1.0], [163, 55, 1.0], [164, 55, 1.0], [149, 56, 1.0], [150, 56, 1.0], [151, 56, 1.0], [152, 56, 1.0], [153, 56, 1.0], [154, 56, 1.0], [155, 56, 1.0], [156, 56, 1.0], [157, 56, 1.0], [158, 56, 1.0], [159, 56, 1.0], [160, 56, 1.0], [161, 56, 1.0], [162, 56, 1.0], [163, 56, 1.0], [164, 56, 1.0], [148, 57, 1.0], [149, 57, 1.0], [150, 57, 1.0], [151, 57, 1.0], [152, 57, 1.0], [153, 57, 1.0], [154, 57, 1.0], [155, 57, 1.0], [156, 57, 1.0], [157, 57, 1.0], [158, 57, 1.0], [159, 57, 1.0], [160, 57, 1.0], [161, 57, 1.0], [162, 57, 1.0], [163, 57, 1.0], [164, 57, 1.0], [165, 57, 1.0], [148, 58, 1.0], [149, 58, 1.0], [150, 58, 1.0], [151, 58, 1.0], [152, 58, 1.0], [153, 58, 1.0], [154, 58, 1.0], [155, 58, 1.0], [156, 58, 1.0], [157, 58, 1.0], [158, 58, 1.0], [159, 58, 1.0], ...] |
| 1 | [[136, 63, 1.0], [137, 63, 1.0], [138, 63, 1.0], [139, 63, 1.0], [140, 63, 1.0], [141, 63, 1.0], [135, 64, 1.0], [136, 64, 1.0], [137, 64, 1.0], [138, 64, 1.0], [139, 64, 1.0], [140, 64, 1.0], [141, 64, 1.0], [142, 64, 1.0], [143, 64, 1.0], [134, 65, 1.0], [135, 65, 1.0], [136, 65, 1.0], [137, 65, 1.0], [138, 65, 1.0], [139, 65, 1.0], [140, 65, 1.0], [141, 65, 1.0], [142, 65, 1.0], [143, 65, 1.0], [133, 66, 1.0], [134, 66, 1.0], [135, 66, 1.0], [136, 66, 1.0], [137, 66, 1.0], [138, 66, 1.0], [139, 66, 1.0], [140, 66, 1.0], [141, 66, 1.0], [142, 66, 1.0], [143, 66, 1.0], [144, 66, 1.0], [133, 67, 1.0], [134, 67, 1.0], [135, 67, 1.0], [136, 67, 1.0], [137, 67, 1.0], [138, 67, 1.0], [139, 67, 1.0], [140, 67, 1.0], [141, 67, 1.0], [142, 67, 1.0], [143, 67, 1.0], [144, 67, 1.0], [145, 67, 1.0], [133, 68, 1.0], [134, 68, 1.0], [135, 68, 1.0], [136, 68, 1.0], [137, 68, 1.0], [138, 68, 1.0], [139, 68, 1.0], [140, 68, 1.0], [141, 68, 1.0], [142, 68, 1.0], [143, 68, 1.0], [144, 68, 1.0], [145, 68, 1.0], [132, 69, 1.0], [133, 69, 1.0], [134, 69, 1.0], [135, 69, 1.0], [136, 69, 1.0], [137, 69, 1.0], [138, 69, 1.0], [139, 69, 1.0], [140, 69, 1.0], [141, 69, 1.0], [142, 69, 1.0], [143, 69, 1.0], [144, 69, 1.0], [145, 69, 1.0], [146, 69, 1.0], [132, 70, 1.0], [133, 70, 1.0], [134, 70, 1.0], [135, 70, 1.0], [136, 70, 1.0], [137, 70, 1.0], [138, 70, 1.0], [139, 70, 1.0], [140, 70, 1.0], [141, 70, 1.0], [142, 70, 1.0], [143, 70, 1.0], [144, 70, 1.0], [145, 70, 1.0], [146, 70, 1.0], [147, 70, 1.0], [132, 71, 1.0], [133, 71, 1.0], [134, 71, 1.0], [135, 71, 1.0], [136, 71, 1.0], [137, 71, 1.0], ...] |
| 2 | [[144, 96, 1.0], [145, 96, 1.0], [150, 96, 1.0], [151, 96, 1.0], [142, 97, 1.0], [143, 97, 1.0], [144, 97, 1.0], [145, 97, 1.0], [146, 97, 1.0], [147, 97, 1.0], [148, 97, 1.0], [149, 97, 1.0], [150, 97, 1.0], [151, 97, 1.0], [152, 97, 1.0], [140, 98, 1.0], [141, 98, 1.0], [142, 98, 1.0], [143, 98, 1.0], [144, 98, 1.0], [145, 98, 1.0], [146, 98, 1.0], [147, 98, 1.0], [148, 98, 1.0], [149, 98, 1.0], [150, 98, 1.0], [151, 98, 1.0], [152, 98, 1.0], [153, 98, 1.0], [139, 99, 1.0], [140, 99, 1.0], [141, 99, 1.0], [142, 99, 1.0], [143, 99, 1.0], [144, 99, 1.0], [145, 99, 1.0], [146, 99, 1.0], [147, 99, 1.0], [148, 99, 1.0], [149, 99, 1.0], [150, 99, 1.0], [151, 99, 1.0], [152, 99, 1.0], [153, 99, 1.0], [139, 100, 1.0], [140, 100, 1.0], [141, 100, 1.0], [142, 100, 1.0], [143, 100, 1.0], [144, 100, 1.0], [145, 100, 1.0], [146, 100, 1.0], [147, 100, 1.0], [148, 100, 1.0], [149, 100, 1.0], [150, 100, 1.0], [151, 100, 1.0], [152, 100, 1.0], [153, 100, 1.0], [139, 101, 1.0], [140, 101, 1.0], [141, 101, 1.0], [142, 101, 1.0], [143, 101, 1.0], [144, 101, 1.0], [145, 101, 1.0], [146, 101, 1.0], [147, 101, 1.0], [148, 101, 1.0], [149, 101, 1.0], [150, 101, 1.0], [151, 101, 1.0], [152, 101, 1.0], [153, 101, 1.0], [140, 102, 1.0], [141, 102, 1.0], [142, 102, 1.0], [143, 102, 1.0], [144, 102, 1.0], [145, 102, 1.0], [146, 102, 1.0], [147, 102, 1.0], [148, 102, 1.0], [149, 102, 1.0], [150, 102, 1.0], [151, 102, 1.0], [152, 102, 1.0], [142, 103, 1.0], [143, 103, 1.0], [144, 103, 1.0], [145, 103, 1.0], [146, 103, 1.0], [147, 103, 1.0], [148, 103, 1.0], [149, 103, 1.0], [150, 103, 1.0], [151, 103, 1.0], [143, 104, 1.0], [144, 104, 1.0], [145, 104, 1.0], ...] |
| 3 | [[146, 85, 1.0], [144, 86, 1.0], [145, 86, 1.0], [146, 86, 1.0], [147, 86, 1.0], [148, 86, 1.0], [149, 86, 1.0], [143, 87, 1.0], [144, 87, 1.0], [145, 87, 1.0], [146, 87, 1.0], [147, 87, 1.0], [148, 87, 1.0], [149, 87, 1.0], [150, 87, 1.0], [142, 88, 1.0], [143, 88, 1.0], [144, 88, 1.0], [145, 88, 1.0], [146, 88, 1.0], [147, 88, 1.0], [148, 88, 1.0], [149, 88, 1.0], [150, 88, 1.0], [142, 89, 1.0], [143, 89, 1.0], [144, 89, 1.0], [145, 89, 1.0], [146, 89, 1.0], [147, 89, 1.0], [148, 89, 1.0], [149, 89, 1.0], [150, 89, 1.0], [151, 89, 1.0], [141, 90, 1.0], [142, 90, 1.0], [143, 90, 1.0], [144, 90, 1.0], [145, 90, 1.0], [146, 90, 1.0], [147, 90, 1.0], [148, 90, 1.0], [149, 90, 1.0], [150, 90, 1.0], [151, 90, 1.0], [152, 90, 1.0], [141, 91, 1.0], [142, 91, 1.0], [143, 91, 1.0], [144, 91, 1.0], [145, 91, 1.0], [146, 91, 1.0], [147, 91, 1.0], [148, 91, 1.0], [149, 91, 1.0], [150, 91, 1.0], [151, 91, 1.0], [152, 91, 1.0], [142, 92, 1.0], [143, 92, 1.0], [144, 92, 1.0], [145, 92, 1.0], [146, 92, 1.0], [147, 92, 1.0], [148, 92, 1.0], [149, 92, 1.0], [150, 92, 1.0], [151, 92, 1.0], [152, 92, 1.0], [142, 93, 1.0], [143, 93, 1.0], [144, 93, 1.0], [145, 93, 1.0], [146, 93, 1.0], [147, 93, 1.0], [148, 93, 1.0], [149, 93, 1.0], [150, 93, 1.0], [151, 93, 1.0], [152, 93, 1.0], [143, 94, 1.0], [144, 94, 1.0], [145, 94, 1.0], [146, 94, 1.0], [147, 94, 1.0], [148, 94, 1.0], [149, 94, 1.0], [150, 94, 1.0], [151, 94, 1.0], [144, 95, 1.0], [145, 95, 1.0], [146, 95, 1.0], [147, 95, 1.0], [148, 95, 1.0], [149, 95, 1.0], [150, 95, 1.0], [151, 95, 1.0], [146, 96, 1.0], [147, 96, 1.0], [148, 96, 1.0], ...] |
... and 44 more rows.
fluorescence_FOV3_channel1
data
timestamps
rois
table
imaging_plane
optical_channel
0
device
table
| pixel_mask | |
|---|---|
| id | |
| 0 | [[335, 89, 1.0], [332, 90, 1.0], [333, 90, 1.0], [334, 90, 1.0], [335, 90, 1.0], [336, 90, 1.0], [337, 90, 1.0], [338, 90, 1.0], [339, 90, 1.0], [327, 91, 1.0], [328, 91, 1.0], [329, 91, 1.0], [330, 91, 1.0], [331, 91, 1.0], [332, 91, 1.0], [333, 91, 1.0], [334, 91, 1.0], [335, 91, 1.0], [336, 91, 1.0], [337, 91, 1.0], [338, 91, 1.0], [339, 91, 1.0], [340, 91, 1.0], [326, 92, 1.0], [327, 92, 1.0], [328, 92, 1.0], [329, 92, 1.0], [330, 92, 1.0], [331, 92, 1.0], [332, 92, 1.0], [333, 92, 1.0], [334, 92, 1.0], [335, 92, 1.0], [336, 92, 1.0], [337, 92, 1.0], [338, 92, 1.0], [339, 92, 1.0], [340, 92, 1.0], [341, 92, 1.0], [324, 93, 1.0], [325, 93, 1.0], [326, 93, 1.0], [327, 93, 1.0], [328, 93, 1.0], [329, 93, 1.0], [330, 93, 1.0], [331, 93, 1.0], [332, 93, 1.0], [333, 93, 1.0], [334, 93, 1.0], [335, 93, 1.0], [336, 93, 1.0], [337, 93, 1.0], [338, 93, 1.0], [339, 93, 1.0], [340, 93, 1.0], [341, 93, 1.0], [342, 93, 1.0], [323, 94, 1.0], [324, 94, 1.0], [325, 94, 1.0], [326, 94, 1.0], [327, 94, 1.0], [328, 94, 1.0], [329, 94, 1.0], [330, 94, 1.0], [331, 94, 1.0], [332, 94, 1.0], [333, 94, 1.0], [334, 94, 1.0], [335, 94, 1.0], [336, 94, 1.0], [337, 94, 1.0], [338, 94, 1.0], [339, 94, 1.0], [340, 94, 1.0], [341, 94, 1.0], [342, 94, 1.0], [322, 95, 1.0], [323, 95, 1.0], [324, 95, 1.0], [325, 95, 1.0], [326, 95, 1.0], [327, 95, 1.0], [328, 95, 1.0], [329, 95, 1.0], [330, 95, 1.0], [331, 95, 1.0], [332, 95, 1.0], [333, 95, 1.0], [334, 95, 1.0], [335, 95, 1.0], [336, 95, 1.0], [337, 95, 1.0], [338, 95, 1.0], [339, 95, 1.0], [340, 95, 1.0], [341, 95, 1.0], [342, 95, 1.0], [343, 95, 1.0], ...] |
| 1 | [[325, 77, 1.0], [326, 77, 1.0], [327, 77, 1.0], [328, 77, 1.0], [329, 77, 1.0], [323, 78, 1.0], [324, 78, 1.0], [325, 78, 1.0], [326, 78, 1.0], [327, 78, 1.0], [328, 78, 1.0], [329, 78, 1.0], [330, 78, 1.0], [321, 79, 1.0], [322, 79, 1.0], [323, 79, 1.0], [324, 79, 1.0], [325, 79, 1.0], [326, 79, 1.0], [327, 79, 1.0], [328, 79, 1.0], [329, 79, 1.0], [330, 79, 1.0], [331, 79, 1.0], [320, 80, 1.0], [321, 80, 1.0], [322, 80, 1.0], [323, 80, 1.0], [324, 80, 1.0], [325, 80, 1.0], [326, 80, 1.0], [327, 80, 1.0], [328, 80, 1.0], [329, 80, 1.0], [330, 80, 1.0], [331, 80, 1.0], [332, 80, 1.0], [319, 81, 1.0], [320, 81, 1.0], [321, 81, 1.0], [322, 81, 1.0], [323, 81, 1.0], [324, 81, 1.0], [325, 81, 1.0], [326, 81, 1.0], [327, 81, 1.0], [328, 81, 1.0], [329, 81, 1.0], [330, 81, 1.0], [331, 81, 1.0], [332, 81, 1.0], [319, 82, 1.0], [320, 82, 1.0], [321, 82, 1.0], [322, 82, 1.0], [323, 82, 1.0], [324, 82, 1.0], [325, 82, 1.0], [326, 82, 1.0], [327, 82, 1.0], [328, 82, 1.0], [329, 82, 1.0], [330, 82, 1.0], [331, 82, 1.0], [332, 82, 1.0], [333, 82, 1.0], [318, 83, 1.0], [319, 83, 1.0], [320, 83, 1.0], [321, 83, 1.0], [322, 83, 1.0], [323, 83, 1.0], [324, 83, 1.0], [325, 83, 1.0], [326, 83, 1.0], [327, 83, 1.0], [328, 83, 1.0], [329, 83, 1.0], [330, 83, 1.0], [331, 83, 1.0], [332, 83, 1.0], [333, 83, 1.0], [334, 83, 1.0], [318, 84, 1.0], [319, 84, 1.0], [320, 84, 1.0], [321, 84, 1.0], [322, 84, 1.0], [323, 84, 1.0], [324, 84, 1.0], [325, 84, 1.0], [326, 84, 1.0], [327, 84, 1.0], [328, 84, 1.0], [329, 84, 1.0], [330, 84, 1.0], [331, 84, 1.0], [332, 84, 1.0], [333, 84, 1.0], [334, 84, 1.0], ...] |
| 2 | [[351, 92, 1.0], [352, 92, 1.0], [353, 92, 1.0], [354, 92, 1.0], [355, 92, 1.0], [349, 93, 1.0], [350, 93, 1.0], [351, 93, 1.0], [352, 93, 1.0], [353, 93, 1.0], [354, 93, 1.0], [355, 93, 1.0], [356, 93, 1.0], [357, 93, 1.0], [347, 94, 1.0], [348, 94, 1.0], [349, 94, 1.0], [350, 94, 1.0], [351, 94, 1.0], [352, 94, 1.0], [353, 94, 1.0], [354, 94, 1.0], [355, 94, 1.0], [356, 94, 1.0], [357, 94, 1.0], [358, 94, 1.0], [347, 95, 1.0], [348, 95, 1.0], [349, 95, 1.0], [350, 95, 1.0], [351, 95, 1.0], [352, 95, 1.0], [353, 95, 1.0], [354, 95, 1.0], [355, 95, 1.0], [356, 95, 1.0], [357, 95, 1.0], [358, 95, 1.0], [359, 95, 1.0], [346, 96, 1.0], [347, 96, 1.0], [348, 96, 1.0], [349, 96, 1.0], [350, 96, 1.0], [351, 96, 1.0], [352, 96, 1.0], [353, 96, 1.0], [354, 96, 1.0], [355, 96, 1.0], [356, 96, 1.0], [357, 96, 1.0], [358, 96, 1.0], [359, 96, 1.0], [360, 96, 1.0], [345, 97, 1.0], [346, 97, 1.0], [347, 97, 1.0], [348, 97, 1.0], [349, 97, 1.0], [350, 97, 1.0], [351, 97, 1.0], [352, 97, 1.0], [353, 97, 1.0], [354, 97, 1.0], [355, 97, 1.0], [356, 97, 1.0], [357, 97, 1.0], [358, 97, 1.0], [359, 97, 1.0], [360, 97, 1.0], [361, 97, 1.0], [344, 98, 1.0], [345, 98, 1.0], [346, 98, 1.0], [347, 98, 1.0], [348, 98, 1.0], [349, 98, 1.0], [350, 98, 1.0], [351, 98, 1.0], [352, 98, 1.0], [353, 98, 1.0], [354, 98, 1.0], [355, 98, 1.0], [356, 98, 1.0], [357, 98, 1.0], [358, 98, 1.0], [359, 98, 1.0], [360, 98, 1.0], [361, 98, 1.0], [362, 98, 1.0], [344, 99, 1.0], [345, 99, 1.0], [346, 99, 1.0], [347, 99, 1.0], [348, 99, 1.0], [349, 99, 1.0], [350, 99, 1.0], [351, 99, 1.0], [352, 99, 1.0], [353, 99, 1.0], ...] |
| 3 | [[296, 90, 1.0], [297, 90, 1.0], [293, 91, 1.0], [294, 91, 1.0], [295, 91, 1.0], [296, 91, 1.0], [297, 91, 1.0], [298, 91, 1.0], [299, 91, 1.0], [300, 91, 1.0], [291, 92, 1.0], [292, 92, 1.0], [293, 92, 1.0], [294, 92, 1.0], [295, 92, 1.0], [296, 92, 1.0], [297, 92, 1.0], [298, 92, 1.0], [299, 92, 1.0], [300, 92, 1.0], [301, 92, 1.0], [289, 93, 1.0], [290, 93, 1.0], [291, 93, 1.0], [292, 93, 1.0], [293, 93, 1.0], [294, 93, 1.0], [295, 93, 1.0], [296, 93, 1.0], [297, 93, 1.0], [298, 93, 1.0], [299, 93, 1.0], [300, 93, 1.0], [301, 93, 1.0], [302, 93, 1.0], [288, 94, 1.0], [289, 94, 1.0], [290, 94, 1.0], [291, 94, 1.0], [292, 94, 1.0], [293, 94, 1.0], [294, 94, 1.0], [295, 94, 1.0], [296, 94, 1.0], [297, 94, 1.0], [298, 94, 1.0], [299, 94, 1.0], [300, 94, 1.0], [301, 94, 1.0], [302, 94, 1.0], [287, 95, 1.0], [288, 95, 1.0], [289, 95, 1.0], [290, 95, 1.0], [291, 95, 1.0], [292, 95, 1.0], [293, 95, 1.0], [294, 95, 1.0], [295, 95, 1.0], [296, 95, 1.0], [297, 95, 1.0], [298, 95, 1.0], [299, 95, 1.0], [300, 95, 1.0], [301, 95, 1.0], [302, 95, 1.0], [303, 95, 1.0], [286, 96, 1.0], [287, 96, 1.0], [288, 96, 1.0], [289, 96, 1.0], [290, 96, 1.0], [291, 96, 1.0], [292, 96, 1.0], [293, 96, 1.0], [294, 96, 1.0], [295, 96, 1.0], [296, 96, 1.0], [297, 96, 1.0], [298, 96, 1.0], [299, 96, 1.0], [300, 96, 1.0], [301, 96, 1.0], [302, 96, 1.0], [303, 96, 1.0], [286, 97, 1.0], [287, 97, 1.0], [288, 97, 1.0], [289, 97, 1.0], [290, 97, 1.0], [291, 97, 1.0], [292, 97, 1.0], [293, 97, 1.0], [294, 97, 1.0], [295, 97, 1.0], [296, 97, 1.0], [297, 97, 1.0], [298, 97, 1.0], [299, 97, 1.0], [300, 97, 1.0], ...] |
... and 4 more rows.
image_segmentation
plane_segmentations
plane_segmentation_FOV1_channel1
imaging_plane
optical_channel
0
device
table
| pixel_mask | |
|---|---|
| id | |
| 0 | [[150, 83, 1.0], [151, 83, 1.0], [152, 83, 1.0], [153, 83, 1.0], [154, 83, 1.0], [155, 83, 1.0], [156, 83, 1.0], [157, 83, 1.0], [158, 83, 1.0], [159, 83, 1.0], [160, 83, 1.0], [161, 83, 1.0], [149, 84, 1.0], [150, 84, 1.0], [151, 84, 1.0], [152, 84, 1.0], [153, 84, 1.0], [154, 84, 1.0], [155, 84, 1.0], [156, 84, 1.0], [157, 84, 1.0], [158, 84, 1.0], [159, 84, 1.0], [160, 84, 1.0], [161, 84, 1.0], [162, 84, 1.0], [163, 84, 1.0], [147, 85, 1.0], [148, 85, 1.0], [149, 85, 1.0], [150, 85, 1.0], [151, 85, 1.0], [152, 85, 1.0], [153, 85, 1.0], [154, 85, 1.0], [155, 85, 1.0], [156, 85, 1.0], [157, 85, 1.0], [158, 85, 1.0], [159, 85, 1.0], [160, 85, 1.0], [161, 85, 1.0], [162, 85, 1.0], [163, 85, 1.0], [164, 85, 1.0], [147, 86, 1.0], [148, 86, 1.0], [149, 86, 1.0], [150, 86, 1.0], [151, 86, 1.0], [152, 86, 1.0], [153, 86, 1.0], [154, 86, 1.0], [155, 86, 1.0], [156, 86, 1.0], [157, 86, 1.0], [158, 86, 1.0], [159, 86, 1.0], [160, 86, 1.0], [161, 86, 1.0], [162, 86, 1.0], [163, 86, 1.0], [164, 86, 1.0], [146, 87, 1.0], [147, 87, 1.0], [148, 87, 1.0], [149, 87, 1.0], [150, 87, 1.0], [151, 87, 1.0], [152, 87, 1.0], [153, 87, 1.0], [154, 87, 1.0], [155, 87, 1.0], [156, 87, 1.0], [157, 87, 1.0], [158, 87, 1.0], [159, 87, 1.0], [160, 87, 1.0], [161, 87, 1.0], [162, 87, 1.0], [163, 87, 1.0], [164, 87, 1.0], [147, 88, 1.0], [148, 88, 1.0], [149, 88, 1.0], [150, 88, 1.0], [151, 88, 1.0], [152, 88, 1.0], [153, 88, 1.0], [154, 88, 1.0], [155, 88, 1.0], [156, 88, 1.0], [157, 88, 1.0], [158, 88, 1.0], [159, 88, 1.0], [160, 88, 1.0], [161, 88, 1.0], [162, 88, 1.0], [163, 88, 1.0], [148, 89, 1.0], ...] |
| 1 | [[152, 91, 1.0], [153, 91, 1.0], [154, 91, 1.0], [155, 91, 1.0], [156, 91, 1.0], [150, 92, 1.0], [151, 92, 1.0], [152, 92, 1.0], [153, 92, 1.0], [154, 92, 1.0], [155, 92, 1.0], [156, 92, 1.0], [157, 92, 1.0], [149, 93, 1.0], [150, 93, 1.0], [151, 93, 1.0], [152, 93, 1.0], [153, 93, 1.0], [154, 93, 1.0], [155, 93, 1.0], [156, 93, 1.0], [157, 93, 1.0], [158, 93, 1.0], [148, 94, 1.0], [149, 94, 1.0], [150, 94, 1.0], [151, 94, 1.0], [152, 94, 1.0], [153, 94, 1.0], [154, 94, 1.0], [155, 94, 1.0], [156, 94, 1.0], [157, 94, 1.0], [158, 94, 1.0], [159, 94, 1.0], [148, 95, 1.0], [149, 95, 1.0], [150, 95, 1.0], [151, 95, 1.0], [152, 95, 1.0], [153, 95, 1.0], [154, 95, 1.0], [155, 95, 1.0], [156, 95, 1.0], [157, 95, 1.0], [158, 95, 1.0], [159, 95, 1.0], [160, 95, 1.0], [148, 96, 1.0], [149, 96, 1.0], [150, 96, 1.0], [151, 96, 1.0], [152, 96, 1.0], [153, 96, 1.0], [154, 96, 1.0], [155, 96, 1.0], [156, 96, 1.0], [157, 96, 1.0], [158, 96, 1.0], [159, 96, 1.0], [160, 96, 1.0], [147, 97, 1.0], [148, 97, 1.0], [149, 97, 1.0], [150, 97, 1.0], [151, 97, 1.0], [152, 97, 1.0], [153, 97, 1.0], [154, 97, 1.0], [155, 97, 1.0], [156, 97, 1.0], [157, 97, 1.0], [158, 97, 1.0], [159, 97, 1.0], [160, 97, 1.0], [161, 97, 1.0], [147, 98, 1.0], [148, 98, 1.0], [149, 98, 1.0], [150, 98, 1.0], [151, 98, 1.0], [152, 98, 1.0], [153, 98, 1.0], [154, 98, 1.0], [155, 98, 1.0], [156, 98, 1.0], [157, 98, 1.0], [158, 98, 1.0], [159, 98, 1.0], [160, 98, 1.0], [161, 98, 1.0], [148, 99, 1.0], [149, 99, 1.0], [150, 99, 1.0], [151, 99, 1.0], [152, 99, 1.0], [153, 99, 1.0], [154, 99, 1.0], [155, 99, 1.0], [156, 99, 1.0], ...] |
| 2 | [[145, 100, 1.0], [146, 100, 1.0], [147, 100, 1.0], [143, 101, 1.0], [144, 101, 1.0], [145, 101, 1.0], [146, 101, 1.0], [147, 101, 1.0], [148, 101, 1.0], [149, 101, 1.0], [142, 102, 1.0], [143, 102, 1.0], [144, 102, 1.0], [145, 102, 1.0], [146, 102, 1.0], [147, 102, 1.0], [148, 102, 1.0], [149, 102, 1.0], [150, 102, 1.0], [141, 103, 1.0], [142, 103, 1.0], [143, 103, 1.0], [144, 103, 1.0], [145, 103, 1.0], [146, 103, 1.0], [147, 103, 1.0], [148, 103, 1.0], [149, 103, 1.0], [150, 103, 1.0], [151, 103, 1.0], [140, 104, 1.0], [141, 104, 1.0], [142, 104, 1.0], [143, 104, 1.0], [144, 104, 1.0], [145, 104, 1.0], [146, 104, 1.0], [147, 104, 1.0], [148, 104, 1.0], [149, 104, 1.0], [150, 104, 1.0], [151, 104, 1.0], [152, 104, 1.0], [140, 105, 1.0], [141, 105, 1.0], [142, 105, 1.0], [143, 105, 1.0], [144, 105, 1.0], [145, 105, 1.0], [146, 105, 1.0], [147, 105, 1.0], [148, 105, 1.0], [149, 105, 1.0], [150, 105, 1.0], [151, 105, 1.0], [152, 105, 1.0], [139, 106, 1.0], [140, 106, 1.0], [141, 106, 1.0], [142, 106, 1.0], [143, 106, 1.0], [144, 106, 1.0], [145, 106, 1.0], [146, 106, 1.0], [147, 106, 1.0], [148, 106, 1.0], [149, 106, 1.0], [150, 106, 1.0], [151, 106, 1.0], [152, 106, 1.0], [139, 107, 1.0], [140, 107, 1.0], [141, 107, 1.0], [142, 107, 1.0], [143, 107, 1.0], [144, 107, 1.0], [145, 107, 1.0], [146, 107, 1.0], [147, 107, 1.0], [148, 107, 1.0], [149, 107, 1.0], [150, 107, 1.0], [151, 107, 1.0], [152, 107, 1.0], [139, 108, 1.0], [140, 108, 1.0], [141, 108, 1.0], [142, 108, 1.0], [143, 108, 1.0], [144, 108, 1.0], [145, 108, 1.0], [146, 108, 1.0], [147, 108, 1.0], [148, 108, 1.0], [149, 108, 1.0], [150, 108, 1.0], [151, 108, 1.0], [152, 108, 1.0], [140, 109, 1.0], [141, 109, 1.0], ...] |
| 3 | [[138, 90, 1.0], [139, 90, 1.0], [140, 90, 1.0], [137, 91, 1.0], [138, 91, 1.0], [139, 91, 1.0], [140, 91, 1.0], [141, 91, 1.0], [136, 92, 1.0], [137, 92, 1.0], [138, 92, 1.0], [139, 92, 1.0], [140, 92, 1.0], [141, 92, 1.0], [142, 92, 1.0], [143, 92, 1.0], [135, 93, 1.0], [136, 93, 1.0], [137, 93, 1.0], [138, 93, 1.0], [139, 93, 1.0], [140, 93, 1.0], [141, 93, 1.0], [142, 93, 1.0], [143, 93, 1.0], [144, 93, 1.0], [134, 94, 1.0], [135, 94, 1.0], [136, 94, 1.0], [137, 94, 1.0], [138, 94, 1.0], [139, 94, 1.0], [140, 94, 1.0], [141, 94, 1.0], [142, 94, 1.0], [143, 94, 1.0], [144, 94, 1.0], [134, 95, 1.0], [135, 95, 1.0], [136, 95, 1.0], [137, 95, 1.0], [138, 95, 1.0], [139, 95, 1.0], [140, 95, 1.0], [141, 95, 1.0], [142, 95, 1.0], [143, 95, 1.0], [144, 95, 1.0], [145, 95, 1.0], [134, 96, 1.0], [135, 96, 1.0], [136, 96, 1.0], [137, 96, 1.0], [138, 96, 1.0], [139, 96, 1.0], [140, 96, 1.0], [141, 96, 1.0], [142, 96, 1.0], [143, 96, 1.0], [144, 96, 1.0], [135, 97, 1.0], [136, 97, 1.0], [137, 97, 1.0], [138, 97, 1.0], [139, 97, 1.0], [140, 97, 1.0], [141, 97, 1.0], [142, 97, 1.0], [143, 97, 1.0], [144, 97, 1.0], [135, 98, 1.0], [136, 98, 1.0], [137, 98, 1.0], [138, 98, 1.0], [139, 98, 1.0], [140, 98, 1.0], [141, 98, 1.0], [142, 98, 1.0], [143, 98, 1.0], [144, 98, 1.0], [136, 99, 1.0], [137, 99, 1.0], [138, 99, 1.0], [139, 99, 1.0], [140, 99, 1.0], [141, 99, 1.0], [142, 99, 1.0], [143, 99, 1.0], [137, 100, 1.0], [138, 100, 1.0], [139, 100, 1.0], [140, 100, 1.0], [141, 100, 1.0], [142, 100, 1.0], [138, 101, 1.0], [139, 101, 1.0], [140, 101, 1.0]] |
... and 13 more rows.
plane_segmentation_FOV2_channel1
imaging_plane
optical_channel
0
device
table
| pixel_mask | |
|---|---|
| id | |
| 0 | [[159, 51, 1.0], [160, 51, 1.0], [154, 52, 1.0], [155, 52, 1.0], [156, 52, 1.0], [157, 52, 1.0], [158, 52, 1.0], [159, 52, 1.0], [160, 52, 1.0], [161, 52, 1.0], [162, 52, 1.0], [151, 53, 1.0], [152, 53, 1.0], [153, 53, 1.0], [154, 53, 1.0], [155, 53, 1.0], [156, 53, 1.0], [157, 53, 1.0], [158, 53, 1.0], [159, 53, 1.0], [160, 53, 1.0], [161, 53, 1.0], [162, 53, 1.0], [163, 53, 1.0], [150, 54, 1.0], [151, 54, 1.0], [152, 54, 1.0], [153, 54, 1.0], [154, 54, 1.0], [155, 54, 1.0], [156, 54, 1.0], [157, 54, 1.0], [158, 54, 1.0], [159, 54, 1.0], [160, 54, 1.0], [161, 54, 1.0], [162, 54, 1.0], [163, 54, 1.0], [149, 55, 1.0], [150, 55, 1.0], [151, 55, 1.0], [152, 55, 1.0], [153, 55, 1.0], [154, 55, 1.0], [155, 55, 1.0], [156, 55, 1.0], [157, 55, 1.0], [158, 55, 1.0], [159, 55, 1.0], [160, 55, 1.0], [161, 55, 1.0], [162, 55, 1.0], [163, 55, 1.0], [164, 55, 1.0], [149, 56, 1.0], [150, 56, 1.0], [151, 56, 1.0], [152, 56, 1.0], [153, 56, 1.0], [154, 56, 1.0], [155, 56, 1.0], [156, 56, 1.0], [157, 56, 1.0], [158, 56, 1.0], [159, 56, 1.0], [160, 56, 1.0], [161, 56, 1.0], [162, 56, 1.0], [163, 56, 1.0], [164, 56, 1.0], [148, 57, 1.0], [149, 57, 1.0], [150, 57, 1.0], [151, 57, 1.0], [152, 57, 1.0], [153, 57, 1.0], [154, 57, 1.0], [155, 57, 1.0], [156, 57, 1.0], [157, 57, 1.0], [158, 57, 1.0], [159, 57, 1.0], [160, 57, 1.0], [161, 57, 1.0], [162, 57, 1.0], [163, 57, 1.0], [164, 57, 1.0], [165, 57, 1.0], [148, 58, 1.0], [149, 58, 1.0], [150, 58, 1.0], [151, 58, 1.0], [152, 58, 1.0], [153, 58, 1.0], [154, 58, 1.0], [155, 58, 1.0], [156, 58, 1.0], [157, 58, 1.0], [158, 58, 1.0], [159, 58, 1.0], ...] |
| 1 | [[136, 63, 1.0], [137, 63, 1.0], [138, 63, 1.0], [139, 63, 1.0], [140, 63, 1.0], [141, 63, 1.0], [135, 64, 1.0], [136, 64, 1.0], [137, 64, 1.0], [138, 64, 1.0], [139, 64, 1.0], [140, 64, 1.0], [141, 64, 1.0], [142, 64, 1.0], [143, 64, 1.0], [134, 65, 1.0], [135, 65, 1.0], [136, 65, 1.0], [137, 65, 1.0], [138, 65, 1.0], [139, 65, 1.0], [140, 65, 1.0], [141, 65, 1.0], [142, 65, 1.0], [143, 65, 1.0], [133, 66, 1.0], [134, 66, 1.0], [135, 66, 1.0], [136, 66, 1.0], [137, 66, 1.0], [138, 66, 1.0], [139, 66, 1.0], [140, 66, 1.0], [141, 66, 1.0], [142, 66, 1.0], [143, 66, 1.0], [144, 66, 1.0], [133, 67, 1.0], [134, 67, 1.0], [135, 67, 1.0], [136, 67, 1.0], [137, 67, 1.0], [138, 67, 1.0], [139, 67, 1.0], [140, 67, 1.0], [141, 67, 1.0], [142, 67, 1.0], [143, 67, 1.0], [144, 67, 1.0], [145, 67, 1.0], [133, 68, 1.0], [134, 68, 1.0], [135, 68, 1.0], [136, 68, 1.0], [137, 68, 1.0], [138, 68, 1.0], [139, 68, 1.0], [140, 68, 1.0], [141, 68, 1.0], [142, 68, 1.0], [143, 68, 1.0], [144, 68, 1.0], [145, 68, 1.0], [132, 69, 1.0], [133, 69, 1.0], [134, 69, 1.0], [135, 69, 1.0], [136, 69, 1.0], [137, 69, 1.0], [138, 69, 1.0], [139, 69, 1.0], [140, 69, 1.0], [141, 69, 1.0], [142, 69, 1.0], [143, 69, 1.0], [144, 69, 1.0], [145, 69, 1.0], [146, 69, 1.0], [132, 70, 1.0], [133, 70, 1.0], [134, 70, 1.0], [135, 70, 1.0], [136, 70, 1.0], [137, 70, 1.0], [138, 70, 1.0], [139, 70, 1.0], [140, 70, 1.0], [141, 70, 1.0], [142, 70, 1.0], [143, 70, 1.0], [144, 70, 1.0], [145, 70, 1.0], [146, 70, 1.0], [147, 70, 1.0], [132, 71, 1.0], [133, 71, 1.0], [134, 71, 1.0], [135, 71, 1.0], [136, 71, 1.0], [137, 71, 1.0], ...] |
| 2 | [[144, 96, 1.0], [145, 96, 1.0], [150, 96, 1.0], [151, 96, 1.0], [142, 97, 1.0], [143, 97, 1.0], [144, 97, 1.0], [145, 97, 1.0], [146, 97, 1.0], [147, 97, 1.0], [148, 97, 1.0], [149, 97, 1.0], [150, 97, 1.0], [151, 97, 1.0], [152, 97, 1.0], [140, 98, 1.0], [141, 98, 1.0], [142, 98, 1.0], [143, 98, 1.0], [144, 98, 1.0], [145, 98, 1.0], [146, 98, 1.0], [147, 98, 1.0], [148, 98, 1.0], [149, 98, 1.0], [150, 98, 1.0], [151, 98, 1.0], [152, 98, 1.0], [153, 98, 1.0], [139, 99, 1.0], [140, 99, 1.0], [141, 99, 1.0], [142, 99, 1.0], [143, 99, 1.0], [144, 99, 1.0], [145, 99, 1.0], [146, 99, 1.0], [147, 99, 1.0], [148, 99, 1.0], [149, 99, 1.0], [150, 99, 1.0], [151, 99, 1.0], [152, 99, 1.0], [153, 99, 1.0], [139, 100, 1.0], [140, 100, 1.0], [141, 100, 1.0], [142, 100, 1.0], [143, 100, 1.0], [144, 100, 1.0], [145, 100, 1.0], [146, 100, 1.0], [147, 100, 1.0], [148, 100, 1.0], [149, 100, 1.0], [150, 100, 1.0], [151, 100, 1.0], [152, 100, 1.0], [153, 100, 1.0], [139, 101, 1.0], [140, 101, 1.0], [141, 101, 1.0], [142, 101, 1.0], [143, 101, 1.0], [144, 101, 1.0], [145, 101, 1.0], [146, 101, 1.0], [147, 101, 1.0], [148, 101, 1.0], [149, 101, 1.0], [150, 101, 1.0], [151, 101, 1.0], [152, 101, 1.0], [153, 101, 1.0], [140, 102, 1.0], [141, 102, 1.0], [142, 102, 1.0], [143, 102, 1.0], [144, 102, 1.0], [145, 102, 1.0], [146, 102, 1.0], [147, 102, 1.0], [148, 102, 1.0], [149, 102, 1.0], [150, 102, 1.0], [151, 102, 1.0], [152, 102, 1.0], [142, 103, 1.0], [143, 103, 1.0], [144, 103, 1.0], [145, 103, 1.0], [146, 103, 1.0], [147, 103, 1.0], [148, 103, 1.0], [149, 103, 1.0], [150, 103, 1.0], [151, 103, 1.0], [143, 104, 1.0], [144, 104, 1.0], [145, 104, 1.0], ...] |
| 3 | [[146, 85, 1.0], [144, 86, 1.0], [145, 86, 1.0], [146, 86, 1.0], [147, 86, 1.0], [148, 86, 1.0], [149, 86, 1.0], [143, 87, 1.0], [144, 87, 1.0], [145, 87, 1.0], [146, 87, 1.0], [147, 87, 1.0], [148, 87, 1.0], [149, 87, 1.0], [150, 87, 1.0], [142, 88, 1.0], [143, 88, 1.0], [144, 88, 1.0], [145, 88, 1.0], [146, 88, 1.0], [147, 88, 1.0], [148, 88, 1.0], [149, 88, 1.0], [150, 88, 1.0], [142, 89, 1.0], [143, 89, 1.0], [144, 89, 1.0], [145, 89, 1.0], [146, 89, 1.0], [147, 89, 1.0], [148, 89, 1.0], [149, 89, 1.0], [150, 89, 1.0], [151, 89, 1.0], [141, 90, 1.0], [142, 90, 1.0], [143, 90, 1.0], [144, 90, 1.0], [145, 90, 1.0], [146, 90, 1.0], [147, 90, 1.0], [148, 90, 1.0], [149, 90, 1.0], [150, 90, 1.0], [151, 90, 1.0], [152, 90, 1.0], [141, 91, 1.0], [142, 91, 1.0], [143, 91, 1.0], [144, 91, 1.0], [145, 91, 1.0], [146, 91, 1.0], [147, 91, 1.0], [148, 91, 1.0], [149, 91, 1.0], [150, 91, 1.0], [151, 91, 1.0], [152, 91, 1.0], [142, 92, 1.0], [143, 92, 1.0], [144, 92, 1.0], [145, 92, 1.0], [146, 92, 1.0], [147, 92, 1.0], [148, 92, 1.0], [149, 92, 1.0], [150, 92, 1.0], [151, 92, 1.0], [152, 92, 1.0], [142, 93, 1.0], [143, 93, 1.0], [144, 93, 1.0], [145, 93, 1.0], [146, 93, 1.0], [147, 93, 1.0], [148, 93, 1.0], [149, 93, 1.0], [150, 93, 1.0], [151, 93, 1.0], [152, 93, 1.0], [143, 94, 1.0], [144, 94, 1.0], [145, 94, 1.0], [146, 94, 1.0], [147, 94, 1.0], [148, 94, 1.0], [149, 94, 1.0], [150, 94, 1.0], [151, 94, 1.0], [144, 95, 1.0], [145, 95, 1.0], [146, 95, 1.0], [147, 95, 1.0], [148, 95, 1.0], [149, 95, 1.0], [150, 95, 1.0], [151, 95, 1.0], [146, 96, 1.0], [147, 96, 1.0], [148, 96, 1.0], ...] |
... and 44 more rows.
plane_segmentation_FOV3_channel1
imaging_plane
optical_channel
0
device
table
| pixel_mask | |
|---|---|
| id | |
| 0 | [[335, 89, 1.0], [332, 90, 1.0], [333, 90, 1.0], [334, 90, 1.0], [335, 90, 1.0], [336, 90, 1.0], [337, 90, 1.0], [338, 90, 1.0], [339, 90, 1.0], [327, 91, 1.0], [328, 91, 1.0], [329, 91, 1.0], [330, 91, 1.0], [331, 91, 1.0], [332, 91, 1.0], [333, 91, 1.0], [334, 91, 1.0], [335, 91, 1.0], [336, 91, 1.0], [337, 91, 1.0], [338, 91, 1.0], [339, 91, 1.0], [340, 91, 1.0], [326, 92, 1.0], [327, 92, 1.0], [328, 92, 1.0], [329, 92, 1.0], [330, 92, 1.0], [331, 92, 1.0], [332, 92, 1.0], [333, 92, 1.0], [334, 92, 1.0], [335, 92, 1.0], [336, 92, 1.0], [337, 92, 1.0], [338, 92, 1.0], [339, 92, 1.0], [340, 92, 1.0], [341, 92, 1.0], [324, 93, 1.0], [325, 93, 1.0], [326, 93, 1.0], [327, 93, 1.0], [328, 93, 1.0], [329, 93, 1.0], [330, 93, 1.0], [331, 93, 1.0], [332, 93, 1.0], [333, 93, 1.0], [334, 93, 1.0], [335, 93, 1.0], [336, 93, 1.0], [337, 93, 1.0], [338, 93, 1.0], [339, 93, 1.0], [340, 93, 1.0], [341, 93, 1.0], [342, 93, 1.0], [323, 94, 1.0], [324, 94, 1.0], [325, 94, 1.0], [326, 94, 1.0], [327, 94, 1.0], [328, 94, 1.0], [329, 94, 1.0], [330, 94, 1.0], [331, 94, 1.0], [332, 94, 1.0], [333, 94, 1.0], [334, 94, 1.0], [335, 94, 1.0], [336, 94, 1.0], [337, 94, 1.0], [338, 94, 1.0], [339, 94, 1.0], [340, 94, 1.0], [341, 94, 1.0], [342, 94, 1.0], [322, 95, 1.0], [323, 95, 1.0], [324, 95, 1.0], [325, 95, 1.0], [326, 95, 1.0], [327, 95, 1.0], [328, 95, 1.0], [329, 95, 1.0], [330, 95, 1.0], [331, 95, 1.0], [332, 95, 1.0], [333, 95, 1.0], [334, 95, 1.0], [335, 95, 1.0], [336, 95, 1.0], [337, 95, 1.0], [338, 95, 1.0], [339, 95, 1.0], [340, 95, 1.0], [341, 95, 1.0], [342, 95, 1.0], [343, 95, 1.0], ...] |
| 1 | [[325, 77, 1.0], [326, 77, 1.0], [327, 77, 1.0], [328, 77, 1.0], [329, 77, 1.0], [323, 78, 1.0], [324, 78, 1.0], [325, 78, 1.0], [326, 78, 1.0], [327, 78, 1.0], [328, 78, 1.0], [329, 78, 1.0], [330, 78, 1.0], [321, 79, 1.0], [322, 79, 1.0], [323, 79, 1.0], [324, 79, 1.0], [325, 79, 1.0], [326, 79, 1.0], [327, 79, 1.0], [328, 79, 1.0], [329, 79, 1.0], [330, 79, 1.0], [331, 79, 1.0], [320, 80, 1.0], [321, 80, 1.0], [322, 80, 1.0], [323, 80, 1.0], [324, 80, 1.0], [325, 80, 1.0], [326, 80, 1.0], [327, 80, 1.0], [328, 80, 1.0], [329, 80, 1.0], [330, 80, 1.0], [331, 80, 1.0], [332, 80, 1.0], [319, 81, 1.0], [320, 81, 1.0], [321, 81, 1.0], [322, 81, 1.0], [323, 81, 1.0], [324, 81, 1.0], [325, 81, 1.0], [326, 81, 1.0], [327, 81, 1.0], [328, 81, 1.0], [329, 81, 1.0], [330, 81, 1.0], [331, 81, 1.0], [332, 81, 1.0], [319, 82, 1.0], [320, 82, 1.0], [321, 82, 1.0], [322, 82, 1.0], [323, 82, 1.0], [324, 82, 1.0], [325, 82, 1.0], [326, 82, 1.0], [327, 82, 1.0], [328, 82, 1.0], [329, 82, 1.0], [330, 82, 1.0], [331, 82, 1.0], [332, 82, 1.0], [333, 82, 1.0], [318, 83, 1.0], [319, 83, 1.0], [320, 83, 1.0], [321, 83, 1.0], [322, 83, 1.0], [323, 83, 1.0], [324, 83, 1.0], [325, 83, 1.0], [326, 83, 1.0], [327, 83, 1.0], [328, 83, 1.0], [329, 83, 1.0], [330, 83, 1.0], [331, 83, 1.0], [332, 83, 1.0], [333, 83, 1.0], [334, 83, 1.0], [318, 84, 1.0], [319, 84, 1.0], [320, 84, 1.0], [321, 84, 1.0], [322, 84, 1.0], [323, 84, 1.0], [324, 84, 1.0], [325, 84, 1.0], [326, 84, 1.0], [327, 84, 1.0], [328, 84, 1.0], [329, 84, 1.0], [330, 84, 1.0], [331, 84, 1.0], [332, 84, 1.0], [333, 84, 1.0], [334, 84, 1.0], ...] |
| 2 | [[351, 92, 1.0], [352, 92, 1.0], [353, 92, 1.0], [354, 92, 1.0], [355, 92, 1.0], [349, 93, 1.0], [350, 93, 1.0], [351, 93, 1.0], [352, 93, 1.0], [353, 93, 1.0], [354, 93, 1.0], [355, 93, 1.0], [356, 93, 1.0], [357, 93, 1.0], [347, 94, 1.0], [348, 94, 1.0], [349, 94, 1.0], [350, 94, 1.0], [351, 94, 1.0], [352, 94, 1.0], [353, 94, 1.0], [354, 94, 1.0], [355, 94, 1.0], [356, 94, 1.0], [357, 94, 1.0], [358, 94, 1.0], [347, 95, 1.0], [348, 95, 1.0], [349, 95, 1.0], [350, 95, 1.0], [351, 95, 1.0], [352, 95, 1.0], [353, 95, 1.0], [354, 95, 1.0], [355, 95, 1.0], [356, 95, 1.0], [357, 95, 1.0], [358, 95, 1.0], [359, 95, 1.0], [346, 96, 1.0], [347, 96, 1.0], [348, 96, 1.0], [349, 96, 1.0], [350, 96, 1.0], [351, 96, 1.0], [352, 96, 1.0], [353, 96, 1.0], [354, 96, 1.0], [355, 96, 1.0], [356, 96, 1.0], [357, 96, 1.0], [358, 96, 1.0], [359, 96, 1.0], [360, 96, 1.0], [345, 97, 1.0], [346, 97, 1.0], [347, 97, 1.0], [348, 97, 1.0], [349, 97, 1.0], [350, 97, 1.0], [351, 97, 1.0], [352, 97, 1.0], [353, 97, 1.0], [354, 97, 1.0], [355, 97, 1.0], [356, 97, 1.0], [357, 97, 1.0], [358, 97, 1.0], [359, 97, 1.0], [360, 97, 1.0], [361, 97, 1.0], [344, 98, 1.0], [345, 98, 1.0], [346, 98, 1.0], [347, 98, 1.0], [348, 98, 1.0], [349, 98, 1.0], [350, 98, 1.0], [351, 98, 1.0], [352, 98, 1.0], [353, 98, 1.0], [354, 98, 1.0], [355, 98, 1.0], [356, 98, 1.0], [357, 98, 1.0], [358, 98, 1.0], [359, 98, 1.0], [360, 98, 1.0], [361, 98, 1.0], [362, 98, 1.0], [344, 99, 1.0], [345, 99, 1.0], [346, 99, 1.0], [347, 99, 1.0], [348, 99, 1.0], [349, 99, 1.0], [350, 99, 1.0], [351, 99, 1.0], [352, 99, 1.0], [353, 99, 1.0], ...] |
| 3 | [[296, 90, 1.0], [297, 90, 1.0], [293, 91, 1.0], [294, 91, 1.0], [295, 91, 1.0], [296, 91, 1.0], [297, 91, 1.0], [298, 91, 1.0], [299, 91, 1.0], [300, 91, 1.0], [291, 92, 1.0], [292, 92, 1.0], [293, 92, 1.0], [294, 92, 1.0], [295, 92, 1.0], [296, 92, 1.0], [297, 92, 1.0], [298, 92, 1.0], [299, 92, 1.0], [300, 92, 1.0], [301, 92, 1.0], [289, 93, 1.0], [290, 93, 1.0], [291, 93, 1.0], [292, 93, 1.0], [293, 93, 1.0], [294, 93, 1.0], [295, 93, 1.0], [296, 93, 1.0], [297, 93, 1.0], [298, 93, 1.0], [299, 93, 1.0], [300, 93, 1.0], [301, 93, 1.0], [302, 93, 1.0], [288, 94, 1.0], [289, 94, 1.0], [290, 94, 1.0], [291, 94, 1.0], [292, 94, 1.0], [293, 94, 1.0], [294, 94, 1.0], [295, 94, 1.0], [296, 94, 1.0], [297, 94, 1.0], [298, 94, 1.0], [299, 94, 1.0], [300, 94, 1.0], [301, 94, 1.0], [302, 94, 1.0], [287, 95, 1.0], [288, 95, 1.0], [289, 95, 1.0], [290, 95, 1.0], [291, 95, 1.0], [292, 95, 1.0], [293, 95, 1.0], [294, 95, 1.0], [295, 95, 1.0], [296, 95, 1.0], [297, 95, 1.0], [298, 95, 1.0], [299, 95, 1.0], [300, 95, 1.0], [301, 95, 1.0], [302, 95, 1.0], [303, 95, 1.0], [286, 96, 1.0], [287, 96, 1.0], [288, 96, 1.0], [289, 96, 1.0], [290, 96, 1.0], [291, 96, 1.0], [292, 96, 1.0], [293, 96, 1.0], [294, 96, 1.0], [295, 96, 1.0], [296, 96, 1.0], [297, 96, 1.0], [298, 96, 1.0], [299, 96, 1.0], [300, 96, 1.0], [301, 96, 1.0], [302, 96, 1.0], [303, 96, 1.0], [286, 97, 1.0], [287, 97, 1.0], [288, 97, 1.0], [289, 97, 1.0], [290, 97, 1.0], [291, 97, 1.0], [292, 97, 1.0], [293, 97, 1.0], [294, 97, 1.0], [295, 97, 1.0], [296, 97, 1.0], [297, 97, 1.0], [298, 97, 1.0], [299, 97, 1.0], [300, 97, 1.0], ...] |
... and 4 more rows.
devices
two_photon_microscope
imaging_planes
imaging_plane_channel1
optical_channel
0
device
intervals
trials
table
| start_time | stop_time | odorant | concentration | solution_date | |
|---|---|---|---|---|---|
| id | |||||
| 0 | 59.2888 | 60.2928 | Methyl Salicylate | 0.1 | 2022-05-17 |
| 1 | 60.2966 | 61.2995 | Methyl Salicylate | 0.1 | 2022-05-17 |
| 2 | 61.3034 | 62.3067 | Methyl Salicylate | 0.1 | 2022-05-17 |
| 3 | 62.3106 | 63.3130 | Methyl Salicylate | 0.1 | 2022-05-17 |
... and 496 more rows.
subject
date_of_birth
2021-07-15 00:00:00+02:00trials
table
| start_time | stop_time | odorant | concentration | solution_date | |
|---|---|---|---|---|---|
| id | |||||
| 0 | 59.2888 | 60.2928 | Methyl Salicylate | 0.1 | 2022-05-17 |
| 1 | 60.2966 | 61.2995 | Methyl Salicylate | 0.1 | 2022-05-17 |
| 2 | 61.3034 | 62.3067 | Methyl Salicylate | 0.1 | 2022-05-17 |
| 3 | 62.3106 | 63.3130 | Methyl Salicylate | 0.1 | 2022-05-17 |
... and 496 more rows.
Importantly, the session start time is the reference time for all timestamps in the file. For instance, an event with a timestamp of 0 in the file means the event occurred exactly at the session start time.
The session_start_time is extracted from all_sessions.Session datajoint table.
nwbfile.session_start_time
datetime.datetime(2022, 7, 21, 0, 0, tzinfo=tzoffset(None, -18000))
The experiment description or the session description can be easily accessed with nwbfile.experiment_description and nwbfile.session_description
nwbfile.experiment_description
'Awake mice were head fixed on a running wheel and presented with odors. A meso-scale two-photon microscope was used to image glomerular activity in the olfactory bulb.'
nwbfile.session_description
'In this study, we explore odor-evoked activity representation in the olfactory bulb (OB) and how odor responses enable odor discrimination. Contrary to some previously cited theories that suggest a sparse representation, we hypothesize a more dense representation during odor presentation. A key question is how odors are reliably encoded in OB activity patterns, and how these patterns contribute to early odor processing. To address this problem, we recorded population level odor responses from the mouse OB with mesoscale two photon calcium imaging and applied machine learning techniques to suggest a model in which sparse coding is largely sufficient for olfaction, but redundant information may make odor coding more robust across different variables.'
nwbfile.subject
subject (Subject)
date_of_birth
2021-07-15 00:00:00+02:00Access TwoPhoton Imaging¶
This section demonstraces how to access the raw Two Photon imaging data.
NWB organizes data into different groups depending on the type of data. Groups can be thought of as folders within the file. Here are some of the groups within an NWBFile and the types of data they are intended to store:
acquisition: raw, acquired data that should never changeprocessing: processed data, typically the results of preprocessing algorithms and could change
Raw TwoPhoton Imaging ¶
The raw TwoPhoton imaging data is stored in pynwb.ophys.TwoPhotonSeries objects (for each channel and plane separately) which is added to nwbfile.acquisition.
The data in TwoPhotonSeries is stored as a three dimensional array: the first dimension is time (frame), the second and third dimensions represent x and y (width by height).
photon_series_names = [photon_series_name for photon_series_name in nwbfile.acquisition.keys() if "two_photon_series" in photon_series_name]
print(photon_series_names)
['two_photon_series_FOV1_channel1', 'two_photon_series_FOV2_channel1', 'two_photon_series_FOV3_channel1']
# Visualize the imaging data.
from matplotlib import pyplot as plt
fig, axs = plt.subplots(nrows=len(photon_series_names), ncols=1, sharex=True, sharey=True)
for ps_index,ps_name in enumerate(photon_series_names):
photon_series = nwbfile.acquisition[ps_name]
axs[ps_index].imshow(photon_series.data[70], cmap="binary")
axs[ps_index].set_title(ps_name.replace("_"," "))
plt.show()
Imaging metadata include information on the device used to acquire the image and the optical channel specs contained in the imaging plane object
nwbfile.devices["two_photon_microscope"]
two_photon_microscope (Device)
nwbfile.imaging_planes["imaging_plane_channel1"]
imaging_plane_channel1 (ImagingPlane)
optical_channel
0
device
Accessing the segmentation data¶
The segmentation output for the Two Photon Imaging data is stored in nwbfile.processing["ophys"].
In NWB, the PlaneSegmentation class stores the detected regions of interest in the TwoPhotonSeries data. The ImageSegmentation can contain multiple PlaneSegmentation tables, so that we can store results of different segmentation algorithms or different segmentation classes.
We can access the plane segmentation for the TwoPhotonSeries data as
nwbfile.processing["ophys"]["ImageSegmentation"]["PlaneSegmentationChannel_number_Plane_number_"].
nwbfile.processing["ophys"]
ophys (ProcessingModule)
data_interfaces
average_images
images
average_image_FOV1_channel1
average_image_FOV2_channel1
average_image_FOV3_channel1
correlation_images
images
correlation_image_FOV1_channel1
correlation_image_FOV2_channel1
correlation_image_FOV3_channel1
fluorescence
roi_response_series
fluorescence_FOV1_channel1
data
timestamps
rois
table
imaging_plane
optical_channel
0
device
table
| pixel_mask | |
|---|---|
| id | |
| 0 | [[150, 83, 1.0], [151, 83, 1.0], [152, 83, 1.0], [153, 83, 1.0], [154, 83, 1.0], [155, 83, 1.0], [156, 83, 1.0], [157, 83, 1.0], [158, 83, 1.0], [159, 83, 1.0], [160, 83, 1.0], [161, 83, 1.0], [149, 84, 1.0], [150, 84, 1.0], [151, 84, 1.0], [152, 84, 1.0], [153, 84, 1.0], [154, 84, 1.0], [155, 84, 1.0], [156, 84, 1.0], [157, 84, 1.0], [158, 84, 1.0], [159, 84, 1.0], [160, 84, 1.0], [161, 84, 1.0], [162, 84, 1.0], [163, 84, 1.0], [147, 85, 1.0], [148, 85, 1.0], [149, 85, 1.0], [150, 85, 1.0], [151, 85, 1.0], [152, 85, 1.0], [153, 85, 1.0], [154, 85, 1.0], [155, 85, 1.0], [156, 85, 1.0], [157, 85, 1.0], [158, 85, 1.0], [159, 85, 1.0], [160, 85, 1.0], [161, 85, 1.0], [162, 85, 1.0], [163, 85, 1.0], [164, 85, 1.0], [147, 86, 1.0], [148, 86, 1.0], [149, 86, 1.0], [150, 86, 1.0], [151, 86, 1.0], [152, 86, 1.0], [153, 86, 1.0], [154, 86, 1.0], [155, 86, 1.0], [156, 86, 1.0], [157, 86, 1.0], [158, 86, 1.0], [159, 86, 1.0], [160, 86, 1.0], [161, 86, 1.0], [162, 86, 1.0], [163, 86, 1.0], [164, 86, 1.0], [146, 87, 1.0], [147, 87, 1.0], [148, 87, 1.0], [149, 87, 1.0], [150, 87, 1.0], [151, 87, 1.0], [152, 87, 1.0], [153, 87, 1.0], [154, 87, 1.0], [155, 87, 1.0], [156, 87, 1.0], [157, 87, 1.0], [158, 87, 1.0], [159, 87, 1.0], [160, 87, 1.0], [161, 87, 1.0], [162, 87, 1.0], [163, 87, 1.0], [164, 87, 1.0], [147, 88, 1.0], [148, 88, 1.0], [149, 88, 1.0], [150, 88, 1.0], [151, 88, 1.0], [152, 88, 1.0], [153, 88, 1.0], [154, 88, 1.0], [155, 88, 1.0], [156, 88, 1.0], [157, 88, 1.0], [158, 88, 1.0], [159, 88, 1.0], [160, 88, 1.0], [161, 88, 1.0], [162, 88, 1.0], [163, 88, 1.0], [148, 89, 1.0], ...] |
| 1 | [[152, 91, 1.0], [153, 91, 1.0], [154, 91, 1.0], [155, 91, 1.0], [156, 91, 1.0], [150, 92, 1.0], [151, 92, 1.0], [152, 92, 1.0], [153, 92, 1.0], [154, 92, 1.0], [155, 92, 1.0], [156, 92, 1.0], [157, 92, 1.0], [149, 93, 1.0], [150, 93, 1.0], [151, 93, 1.0], [152, 93, 1.0], [153, 93, 1.0], [154, 93, 1.0], [155, 93, 1.0], [156, 93, 1.0], [157, 93, 1.0], [158, 93, 1.0], [148, 94, 1.0], [149, 94, 1.0], [150, 94, 1.0], [151, 94, 1.0], [152, 94, 1.0], [153, 94, 1.0], [154, 94, 1.0], [155, 94, 1.0], [156, 94, 1.0], [157, 94, 1.0], [158, 94, 1.0], [159, 94, 1.0], [148, 95, 1.0], [149, 95, 1.0], [150, 95, 1.0], [151, 95, 1.0], [152, 95, 1.0], [153, 95, 1.0], [154, 95, 1.0], [155, 95, 1.0], [156, 95, 1.0], [157, 95, 1.0], [158, 95, 1.0], [159, 95, 1.0], [160, 95, 1.0], [148, 96, 1.0], [149, 96, 1.0], [150, 96, 1.0], [151, 96, 1.0], [152, 96, 1.0], [153, 96, 1.0], [154, 96, 1.0], [155, 96, 1.0], [156, 96, 1.0], [157, 96, 1.0], [158, 96, 1.0], [159, 96, 1.0], [160, 96, 1.0], [147, 97, 1.0], [148, 97, 1.0], [149, 97, 1.0], [150, 97, 1.0], [151, 97, 1.0], [152, 97, 1.0], [153, 97, 1.0], [154, 97, 1.0], [155, 97, 1.0], [156, 97, 1.0], [157, 97, 1.0], [158, 97, 1.0], [159, 97, 1.0], [160, 97, 1.0], [161, 97, 1.0], [147, 98, 1.0], [148, 98, 1.0], [149, 98, 1.0], [150, 98, 1.0], [151, 98, 1.0], [152, 98, 1.0], [153, 98, 1.0], [154, 98, 1.0], [155, 98, 1.0], [156, 98, 1.0], [157, 98, 1.0], [158, 98, 1.0], [159, 98, 1.0], [160, 98, 1.0], [161, 98, 1.0], [148, 99, 1.0], [149, 99, 1.0], [150, 99, 1.0], [151, 99, 1.0], [152, 99, 1.0], [153, 99, 1.0], [154, 99, 1.0], [155, 99, 1.0], [156, 99, 1.0], ...] |
| 2 | [[145, 100, 1.0], [146, 100, 1.0], [147, 100, 1.0], [143, 101, 1.0], [144, 101, 1.0], [145, 101, 1.0], [146, 101, 1.0], [147, 101, 1.0], [148, 101, 1.0], [149, 101, 1.0], [142, 102, 1.0], [143, 102, 1.0], [144, 102, 1.0], [145, 102, 1.0], [146, 102, 1.0], [147, 102, 1.0], [148, 102, 1.0], [149, 102, 1.0], [150, 102, 1.0], [141, 103, 1.0], [142, 103, 1.0], [143, 103, 1.0], [144, 103, 1.0], [145, 103, 1.0], [146, 103, 1.0], [147, 103, 1.0], [148, 103, 1.0], [149, 103, 1.0], [150, 103, 1.0], [151, 103, 1.0], [140, 104, 1.0], [141, 104, 1.0], [142, 104, 1.0], [143, 104, 1.0], [144, 104, 1.0], [145, 104, 1.0], [146, 104, 1.0], [147, 104, 1.0], [148, 104, 1.0], [149, 104, 1.0], [150, 104, 1.0], [151, 104, 1.0], [152, 104, 1.0], [140, 105, 1.0], [141, 105, 1.0], [142, 105, 1.0], [143, 105, 1.0], [144, 105, 1.0], [145, 105, 1.0], [146, 105, 1.0], [147, 105, 1.0], [148, 105, 1.0], [149, 105, 1.0], [150, 105, 1.0], [151, 105, 1.0], [152, 105, 1.0], [139, 106, 1.0], [140, 106, 1.0], [141, 106, 1.0], [142, 106, 1.0], [143, 106, 1.0], [144, 106, 1.0], [145, 106, 1.0], [146, 106, 1.0], [147, 106, 1.0], [148, 106, 1.0], [149, 106, 1.0], [150, 106, 1.0], [151, 106, 1.0], [152, 106, 1.0], [139, 107, 1.0], [140, 107, 1.0], [141, 107, 1.0], [142, 107, 1.0], [143, 107, 1.0], [144, 107, 1.0], [145, 107, 1.0], [146, 107, 1.0], [147, 107, 1.0], [148, 107, 1.0], [149, 107, 1.0], [150, 107, 1.0], [151, 107, 1.0], [152, 107, 1.0], [139, 108, 1.0], [140, 108, 1.0], [141, 108, 1.0], [142, 108, 1.0], [143, 108, 1.0], [144, 108, 1.0], [145, 108, 1.0], [146, 108, 1.0], [147, 108, 1.0], [148, 108, 1.0], [149, 108, 1.0], [150, 108, 1.0], [151, 108, 1.0], [152, 108, 1.0], [140, 109, 1.0], [141, 109, 1.0], ...] |
| 3 | [[138, 90, 1.0], [139, 90, 1.0], [140, 90, 1.0], [137, 91, 1.0], [138, 91, 1.0], [139, 91, 1.0], [140, 91, 1.0], [141, 91, 1.0], [136, 92, 1.0], [137, 92, 1.0], [138, 92, 1.0], [139, 92, 1.0], [140, 92, 1.0], [141, 92, 1.0], [142, 92, 1.0], [143, 92, 1.0], [135, 93, 1.0], [136, 93, 1.0], [137, 93, 1.0], [138, 93, 1.0], [139, 93, 1.0], [140, 93, 1.0], [141, 93, 1.0], [142, 93, 1.0], [143, 93, 1.0], [144, 93, 1.0], [134, 94, 1.0], [135, 94, 1.0], [136, 94, 1.0], [137, 94, 1.0], [138, 94, 1.0], [139, 94, 1.0], [140, 94, 1.0], [141, 94, 1.0], [142, 94, 1.0], [143, 94, 1.0], [144, 94, 1.0], [134, 95, 1.0], [135, 95, 1.0], [136, 95, 1.0], [137, 95, 1.0], [138, 95, 1.0], [139, 95, 1.0], [140, 95, 1.0], [141, 95, 1.0], [142, 95, 1.0], [143, 95, 1.0], [144, 95, 1.0], [145, 95, 1.0], [134, 96, 1.0], [135, 96, 1.0], [136, 96, 1.0], [137, 96, 1.0], [138, 96, 1.0], [139, 96, 1.0], [140, 96, 1.0], [141, 96, 1.0], [142, 96, 1.0], [143, 96, 1.0], [144, 96, 1.0], [135, 97, 1.0], [136, 97, 1.0], [137, 97, 1.0], [138, 97, 1.0], [139, 97, 1.0], [140, 97, 1.0], [141, 97, 1.0], [142, 97, 1.0], [143, 97, 1.0], [144, 97, 1.0], [135, 98, 1.0], [136, 98, 1.0], [137, 98, 1.0], [138, 98, 1.0], [139, 98, 1.0], [140, 98, 1.0], [141, 98, 1.0], [142, 98, 1.0], [143, 98, 1.0], [144, 98, 1.0], [136, 99, 1.0], [137, 99, 1.0], [138, 99, 1.0], [139, 99, 1.0], [140, 99, 1.0], [141, 99, 1.0], [142, 99, 1.0], [143, 99, 1.0], [137, 100, 1.0], [138, 100, 1.0], [139, 100, 1.0], [140, 100, 1.0], [141, 100, 1.0], [142, 100, 1.0], [138, 101, 1.0], [139, 101, 1.0], [140, 101, 1.0]] |
... and 13 more rows.
fluorescence_FOV2_channel1
data
timestamps
rois
table
imaging_plane
optical_channel
0
device
table
| pixel_mask | |
|---|---|
| id | |
| 0 | [[159, 51, 1.0], [160, 51, 1.0], [154, 52, 1.0], [155, 52, 1.0], [156, 52, 1.0], [157, 52, 1.0], [158, 52, 1.0], [159, 52, 1.0], [160, 52, 1.0], [161, 52, 1.0], [162, 52, 1.0], [151, 53, 1.0], [152, 53, 1.0], [153, 53, 1.0], [154, 53, 1.0], [155, 53, 1.0], [156, 53, 1.0], [157, 53, 1.0], [158, 53, 1.0], [159, 53, 1.0], [160, 53, 1.0], [161, 53, 1.0], [162, 53, 1.0], [163, 53, 1.0], [150, 54, 1.0], [151, 54, 1.0], [152, 54, 1.0], [153, 54, 1.0], [154, 54, 1.0], [155, 54, 1.0], [156, 54, 1.0], [157, 54, 1.0], [158, 54, 1.0], [159, 54, 1.0], [160, 54, 1.0], [161, 54, 1.0], [162, 54, 1.0], [163, 54, 1.0], [149, 55, 1.0], [150, 55, 1.0], [151, 55, 1.0], [152, 55, 1.0], [153, 55, 1.0], [154, 55, 1.0], [155, 55, 1.0], [156, 55, 1.0], [157, 55, 1.0], [158, 55, 1.0], [159, 55, 1.0], [160, 55, 1.0], [161, 55, 1.0], [162, 55, 1.0], [163, 55, 1.0], [164, 55, 1.0], [149, 56, 1.0], [150, 56, 1.0], [151, 56, 1.0], [152, 56, 1.0], [153, 56, 1.0], [154, 56, 1.0], [155, 56, 1.0], [156, 56, 1.0], [157, 56, 1.0], [158, 56, 1.0], [159, 56, 1.0], [160, 56, 1.0], [161, 56, 1.0], [162, 56, 1.0], [163, 56, 1.0], [164, 56, 1.0], [148, 57, 1.0], [149, 57, 1.0], [150, 57, 1.0], [151, 57, 1.0], [152, 57, 1.0], [153, 57, 1.0], [154, 57, 1.0], [155, 57, 1.0], [156, 57, 1.0], [157, 57, 1.0], [158, 57, 1.0], [159, 57, 1.0], [160, 57, 1.0], [161, 57, 1.0], [162, 57, 1.0], [163, 57, 1.0], [164, 57, 1.0], [165, 57, 1.0], [148, 58, 1.0], [149, 58, 1.0], [150, 58, 1.0], [151, 58, 1.0], [152, 58, 1.0], [153, 58, 1.0], [154, 58, 1.0], [155, 58, 1.0], [156, 58, 1.0], [157, 58, 1.0], [158, 58, 1.0], [159, 58, 1.0], ...] |
| 1 | [[136, 63, 1.0], [137, 63, 1.0], [138, 63, 1.0], [139, 63, 1.0], [140, 63, 1.0], [141, 63, 1.0], [135, 64, 1.0], [136, 64, 1.0], [137, 64, 1.0], [138, 64, 1.0], [139, 64, 1.0], [140, 64, 1.0], [141, 64, 1.0], [142, 64, 1.0], [143, 64, 1.0], [134, 65, 1.0], [135, 65, 1.0], [136, 65, 1.0], [137, 65, 1.0], [138, 65, 1.0], [139, 65, 1.0], [140, 65, 1.0], [141, 65, 1.0], [142, 65, 1.0], [143, 65, 1.0], [133, 66, 1.0], [134, 66, 1.0], [135, 66, 1.0], [136, 66, 1.0], [137, 66, 1.0], [138, 66, 1.0], [139, 66, 1.0], [140, 66, 1.0], [141, 66, 1.0], [142, 66, 1.0], [143, 66, 1.0], [144, 66, 1.0], [133, 67, 1.0], [134, 67, 1.0], [135, 67, 1.0], [136, 67, 1.0], [137, 67, 1.0], [138, 67, 1.0], [139, 67, 1.0], [140, 67, 1.0], [141, 67, 1.0], [142, 67, 1.0], [143, 67, 1.0], [144, 67, 1.0], [145, 67, 1.0], [133, 68, 1.0], [134, 68, 1.0], [135, 68, 1.0], [136, 68, 1.0], [137, 68, 1.0], [138, 68, 1.0], [139, 68, 1.0], [140, 68, 1.0], [141, 68, 1.0], [142, 68, 1.0], [143, 68, 1.0], [144, 68, 1.0], [145, 68, 1.0], [132, 69, 1.0], [133, 69, 1.0], [134, 69, 1.0], [135, 69, 1.0], [136, 69, 1.0], [137, 69, 1.0], [138, 69, 1.0], [139, 69, 1.0], [140, 69, 1.0], [141, 69, 1.0], [142, 69, 1.0], [143, 69, 1.0], [144, 69, 1.0], [145, 69, 1.0], [146, 69, 1.0], [132, 70, 1.0], [133, 70, 1.0], [134, 70, 1.0], [135, 70, 1.0], [136, 70, 1.0], [137, 70, 1.0], [138, 70, 1.0], [139, 70, 1.0], [140, 70, 1.0], [141, 70, 1.0], [142, 70, 1.0], [143, 70, 1.0], [144, 70, 1.0], [145, 70, 1.0], [146, 70, 1.0], [147, 70, 1.0], [132, 71, 1.0], [133, 71, 1.0], [134, 71, 1.0], [135, 71, 1.0], [136, 71, 1.0], [137, 71, 1.0], ...] |
| 2 | [[144, 96, 1.0], [145, 96, 1.0], [150, 96, 1.0], [151, 96, 1.0], [142, 97, 1.0], [143, 97, 1.0], [144, 97, 1.0], [145, 97, 1.0], [146, 97, 1.0], [147, 97, 1.0], [148, 97, 1.0], [149, 97, 1.0], [150, 97, 1.0], [151, 97, 1.0], [152, 97, 1.0], [140, 98, 1.0], [141, 98, 1.0], [142, 98, 1.0], [143, 98, 1.0], [144, 98, 1.0], [145, 98, 1.0], [146, 98, 1.0], [147, 98, 1.0], [148, 98, 1.0], [149, 98, 1.0], [150, 98, 1.0], [151, 98, 1.0], [152, 98, 1.0], [153, 98, 1.0], [139, 99, 1.0], [140, 99, 1.0], [141, 99, 1.0], [142, 99, 1.0], [143, 99, 1.0], [144, 99, 1.0], [145, 99, 1.0], [146, 99, 1.0], [147, 99, 1.0], [148, 99, 1.0], [149, 99, 1.0], [150, 99, 1.0], [151, 99, 1.0], [152, 99, 1.0], [153, 99, 1.0], [139, 100, 1.0], [140, 100, 1.0], [141, 100, 1.0], [142, 100, 1.0], [143, 100, 1.0], [144, 100, 1.0], [145, 100, 1.0], [146, 100, 1.0], [147, 100, 1.0], [148, 100, 1.0], [149, 100, 1.0], [150, 100, 1.0], [151, 100, 1.0], [152, 100, 1.0], [153, 100, 1.0], [139, 101, 1.0], [140, 101, 1.0], [141, 101, 1.0], [142, 101, 1.0], [143, 101, 1.0], [144, 101, 1.0], [145, 101, 1.0], [146, 101, 1.0], [147, 101, 1.0], [148, 101, 1.0], [149, 101, 1.0], [150, 101, 1.0], [151, 101, 1.0], [152, 101, 1.0], [153, 101, 1.0], [140, 102, 1.0], [141, 102, 1.0], [142, 102, 1.0], [143, 102, 1.0], [144, 102, 1.0], [145, 102, 1.0], [146, 102, 1.0], [147, 102, 1.0], [148, 102, 1.0], [149, 102, 1.0], [150, 102, 1.0], [151, 102, 1.0], [152, 102, 1.0], [142, 103, 1.0], [143, 103, 1.0], [144, 103, 1.0], [145, 103, 1.0], [146, 103, 1.0], [147, 103, 1.0], [148, 103, 1.0], [149, 103, 1.0], [150, 103, 1.0], [151, 103, 1.0], [143, 104, 1.0], [144, 104, 1.0], [145, 104, 1.0], ...] |
| 3 | [[146, 85, 1.0], [144, 86, 1.0], [145, 86, 1.0], [146, 86, 1.0], [147, 86, 1.0], [148, 86, 1.0], [149, 86, 1.0], [143, 87, 1.0], [144, 87, 1.0], [145, 87, 1.0], [146, 87, 1.0], [147, 87, 1.0], [148, 87, 1.0], [149, 87, 1.0], [150, 87, 1.0], [142, 88, 1.0], [143, 88, 1.0], [144, 88, 1.0], [145, 88, 1.0], [146, 88, 1.0], [147, 88, 1.0], [148, 88, 1.0], [149, 88, 1.0], [150, 88, 1.0], [142, 89, 1.0], [143, 89, 1.0], [144, 89, 1.0], [145, 89, 1.0], [146, 89, 1.0], [147, 89, 1.0], [148, 89, 1.0], [149, 89, 1.0], [150, 89, 1.0], [151, 89, 1.0], [141, 90, 1.0], [142, 90, 1.0], [143, 90, 1.0], [144, 90, 1.0], [145, 90, 1.0], [146, 90, 1.0], [147, 90, 1.0], [148, 90, 1.0], [149, 90, 1.0], [150, 90, 1.0], [151, 90, 1.0], [152, 90, 1.0], [141, 91, 1.0], [142, 91, 1.0], [143, 91, 1.0], [144, 91, 1.0], [145, 91, 1.0], [146, 91, 1.0], [147, 91, 1.0], [148, 91, 1.0], [149, 91, 1.0], [150, 91, 1.0], [151, 91, 1.0], [152, 91, 1.0], [142, 92, 1.0], [143, 92, 1.0], [144, 92, 1.0], [145, 92, 1.0], [146, 92, 1.0], [147, 92, 1.0], [148, 92, 1.0], [149, 92, 1.0], [150, 92, 1.0], [151, 92, 1.0], [152, 92, 1.0], [142, 93, 1.0], [143, 93, 1.0], [144, 93, 1.0], [145, 93, 1.0], [146, 93, 1.0], [147, 93, 1.0], [148, 93, 1.0], [149, 93, 1.0], [150, 93, 1.0], [151, 93, 1.0], [152, 93, 1.0], [143, 94, 1.0], [144, 94, 1.0], [145, 94, 1.0], [146, 94, 1.0], [147, 94, 1.0], [148, 94, 1.0], [149, 94, 1.0], [150, 94, 1.0], [151, 94, 1.0], [144, 95, 1.0], [145, 95, 1.0], [146, 95, 1.0], [147, 95, 1.0], [148, 95, 1.0], [149, 95, 1.0], [150, 95, 1.0], [151, 95, 1.0], [146, 96, 1.0], [147, 96, 1.0], [148, 96, 1.0], ...] |
... and 44 more rows.
fluorescence_FOV3_channel1
data
timestamps
rois
table
imaging_plane
optical_channel
0
device
table
| pixel_mask | |
|---|---|
| id | |
| 0 | [[335, 89, 1.0], [332, 90, 1.0], [333, 90, 1.0], [334, 90, 1.0], [335, 90, 1.0], [336, 90, 1.0], [337, 90, 1.0], [338, 90, 1.0], [339, 90, 1.0], [327, 91, 1.0], [328, 91, 1.0], [329, 91, 1.0], [330, 91, 1.0], [331, 91, 1.0], [332, 91, 1.0], [333, 91, 1.0], [334, 91, 1.0], [335, 91, 1.0], [336, 91, 1.0], [337, 91, 1.0], [338, 91, 1.0], [339, 91, 1.0], [340, 91, 1.0], [326, 92, 1.0], [327, 92, 1.0], [328, 92, 1.0], [329, 92, 1.0], [330, 92, 1.0], [331, 92, 1.0], [332, 92, 1.0], [333, 92, 1.0], [334, 92, 1.0], [335, 92, 1.0], [336, 92, 1.0], [337, 92, 1.0], [338, 92, 1.0], [339, 92, 1.0], [340, 92, 1.0], [341, 92, 1.0], [324, 93, 1.0], [325, 93, 1.0], [326, 93, 1.0], [327, 93, 1.0], [328, 93, 1.0], [329, 93, 1.0], [330, 93, 1.0], [331, 93, 1.0], [332, 93, 1.0], [333, 93, 1.0], [334, 93, 1.0], [335, 93, 1.0], [336, 93, 1.0], [337, 93, 1.0], [338, 93, 1.0], [339, 93, 1.0], [340, 93, 1.0], [341, 93, 1.0], [342, 93, 1.0], [323, 94, 1.0], [324, 94, 1.0], [325, 94, 1.0], [326, 94, 1.0], [327, 94, 1.0], [328, 94, 1.0], [329, 94, 1.0], [330, 94, 1.0], [331, 94, 1.0], [332, 94, 1.0], [333, 94, 1.0], [334, 94, 1.0], [335, 94, 1.0], [336, 94, 1.0], [337, 94, 1.0], [338, 94, 1.0], [339, 94, 1.0], [340, 94, 1.0], [341, 94, 1.0], [342, 94, 1.0], [322, 95, 1.0], [323, 95, 1.0], [324, 95, 1.0], [325, 95, 1.0], [326, 95, 1.0], [327, 95, 1.0], [328, 95, 1.0], [329, 95, 1.0], [330, 95, 1.0], [331, 95, 1.0], [332, 95, 1.0], [333, 95, 1.0], [334, 95, 1.0], [335, 95, 1.0], [336, 95, 1.0], [337, 95, 1.0], [338, 95, 1.0], [339, 95, 1.0], [340, 95, 1.0], [341, 95, 1.0], [342, 95, 1.0], [343, 95, 1.0], ...] |
| 1 | [[325, 77, 1.0], [326, 77, 1.0], [327, 77, 1.0], [328, 77, 1.0], [329, 77, 1.0], [323, 78, 1.0], [324, 78, 1.0], [325, 78, 1.0], [326, 78, 1.0], [327, 78, 1.0], [328, 78, 1.0], [329, 78, 1.0], [330, 78, 1.0], [321, 79, 1.0], [322, 79, 1.0], [323, 79, 1.0], [324, 79, 1.0], [325, 79, 1.0], [326, 79, 1.0], [327, 79, 1.0], [328, 79, 1.0], [329, 79, 1.0], [330, 79, 1.0], [331, 79, 1.0], [320, 80, 1.0], [321, 80, 1.0], [322, 80, 1.0], [323, 80, 1.0], [324, 80, 1.0], [325, 80, 1.0], [326, 80, 1.0], [327, 80, 1.0], [328, 80, 1.0], [329, 80, 1.0], [330, 80, 1.0], [331, 80, 1.0], [332, 80, 1.0], [319, 81, 1.0], [320, 81, 1.0], [321, 81, 1.0], [322, 81, 1.0], [323, 81, 1.0], [324, 81, 1.0], [325, 81, 1.0], [326, 81, 1.0], [327, 81, 1.0], [328, 81, 1.0], [329, 81, 1.0], [330, 81, 1.0], [331, 81, 1.0], [332, 81, 1.0], [319, 82, 1.0], [320, 82, 1.0], [321, 82, 1.0], [322, 82, 1.0], [323, 82, 1.0], [324, 82, 1.0], [325, 82, 1.0], [326, 82, 1.0], [327, 82, 1.0], [328, 82, 1.0], [329, 82, 1.0], [330, 82, 1.0], [331, 82, 1.0], [332, 82, 1.0], [333, 82, 1.0], [318, 83, 1.0], [319, 83, 1.0], [320, 83, 1.0], [321, 83, 1.0], [322, 83, 1.0], [323, 83, 1.0], [324, 83, 1.0], [325, 83, 1.0], [326, 83, 1.0], [327, 83, 1.0], [328, 83, 1.0], [329, 83, 1.0], [330, 83, 1.0], [331, 83, 1.0], [332, 83, 1.0], [333, 83, 1.0], [334, 83, 1.0], [318, 84, 1.0], [319, 84, 1.0], [320, 84, 1.0], [321, 84, 1.0], [322, 84, 1.0], [323, 84, 1.0], [324, 84, 1.0], [325, 84, 1.0], [326, 84, 1.0], [327, 84, 1.0], [328, 84, 1.0], [329, 84, 1.0], [330, 84, 1.0], [331, 84, 1.0], [332, 84, 1.0], [333, 84, 1.0], [334, 84, 1.0], ...] |
| 2 | [[351, 92, 1.0], [352, 92, 1.0], [353, 92, 1.0], [354, 92, 1.0], [355, 92, 1.0], [349, 93, 1.0], [350, 93, 1.0], [351, 93, 1.0], [352, 93, 1.0], [353, 93, 1.0], [354, 93, 1.0], [355, 93, 1.0], [356, 93, 1.0], [357, 93, 1.0], [347, 94, 1.0], [348, 94, 1.0], [349, 94, 1.0], [350, 94, 1.0], [351, 94, 1.0], [352, 94, 1.0], [353, 94, 1.0], [354, 94, 1.0], [355, 94, 1.0], [356, 94, 1.0], [357, 94, 1.0], [358, 94, 1.0], [347, 95, 1.0], [348, 95, 1.0], [349, 95, 1.0], [350, 95, 1.0], [351, 95, 1.0], [352, 95, 1.0], [353, 95, 1.0], [354, 95, 1.0], [355, 95, 1.0], [356, 95, 1.0], [357, 95, 1.0], [358, 95, 1.0], [359, 95, 1.0], [346, 96, 1.0], [347, 96, 1.0], [348, 96, 1.0], [349, 96, 1.0], [350, 96, 1.0], [351, 96, 1.0], [352, 96, 1.0], [353, 96, 1.0], [354, 96, 1.0], [355, 96, 1.0], [356, 96, 1.0], [357, 96, 1.0], [358, 96, 1.0], [359, 96, 1.0], [360, 96, 1.0], [345, 97, 1.0], [346, 97, 1.0], [347, 97, 1.0], [348, 97, 1.0], [349, 97, 1.0], [350, 97, 1.0], [351, 97, 1.0], [352, 97, 1.0], [353, 97, 1.0], [354, 97, 1.0], [355, 97, 1.0], [356, 97, 1.0], [357, 97, 1.0], [358, 97, 1.0], [359, 97, 1.0], [360, 97, 1.0], [361, 97, 1.0], [344, 98, 1.0], [345, 98, 1.0], [346, 98, 1.0], [347, 98, 1.0], [348, 98, 1.0], [349, 98, 1.0], [350, 98, 1.0], [351, 98, 1.0], [352, 98, 1.0], [353, 98, 1.0], [354, 98, 1.0], [355, 98, 1.0], [356, 98, 1.0], [357, 98, 1.0], [358, 98, 1.0], [359, 98, 1.0], [360, 98, 1.0], [361, 98, 1.0], [362, 98, 1.0], [344, 99, 1.0], [345, 99, 1.0], [346, 99, 1.0], [347, 99, 1.0], [348, 99, 1.0], [349, 99, 1.0], [350, 99, 1.0], [351, 99, 1.0], [352, 99, 1.0], [353, 99, 1.0], ...] |
| 3 | [[296, 90, 1.0], [297, 90, 1.0], [293, 91, 1.0], [294, 91, 1.0], [295, 91, 1.0], [296, 91, 1.0], [297, 91, 1.0], [298, 91, 1.0], [299, 91, 1.0], [300, 91, 1.0], [291, 92, 1.0], [292, 92, 1.0], [293, 92, 1.0], [294, 92, 1.0], [295, 92, 1.0], [296, 92, 1.0], [297, 92, 1.0], [298, 92, 1.0], [299, 92, 1.0], [300, 92, 1.0], [301, 92, 1.0], [289, 93, 1.0], [290, 93, 1.0], [291, 93, 1.0], [292, 93, 1.0], [293, 93, 1.0], [294, 93, 1.0], [295, 93, 1.0], [296, 93, 1.0], [297, 93, 1.0], [298, 93, 1.0], [299, 93, 1.0], [300, 93, 1.0], [301, 93, 1.0], [302, 93, 1.0], [288, 94, 1.0], [289, 94, 1.0], [290, 94, 1.0], [291, 94, 1.0], [292, 94, 1.0], [293, 94, 1.0], [294, 94, 1.0], [295, 94, 1.0], [296, 94, 1.0], [297, 94, 1.0], [298, 94, 1.0], [299, 94, 1.0], [300, 94, 1.0], [301, 94, 1.0], [302, 94, 1.0], [287, 95, 1.0], [288, 95, 1.0], [289, 95, 1.0], [290, 95, 1.0], [291, 95, 1.0], [292, 95, 1.0], [293, 95, 1.0], [294, 95, 1.0], [295, 95, 1.0], [296, 95, 1.0], [297, 95, 1.0], [298, 95, 1.0], [299, 95, 1.0], [300, 95, 1.0], [301, 95, 1.0], [302, 95, 1.0], [303, 95, 1.0], [286, 96, 1.0], [287, 96, 1.0], [288, 96, 1.0], [289, 96, 1.0], [290, 96, 1.0], [291, 96, 1.0], [292, 96, 1.0], [293, 96, 1.0], [294, 96, 1.0], [295, 96, 1.0], [296, 96, 1.0], [297, 96, 1.0], [298, 96, 1.0], [299, 96, 1.0], [300, 96, 1.0], [301, 96, 1.0], [302, 96, 1.0], [303, 96, 1.0], [286, 97, 1.0], [287, 97, 1.0], [288, 97, 1.0], [289, 97, 1.0], [290, 97, 1.0], [291, 97, 1.0], [292, 97, 1.0], [293, 97, 1.0], [294, 97, 1.0], [295, 97, 1.0], [296, 97, 1.0], [297, 97, 1.0], [298, 97, 1.0], [299, 97, 1.0], [300, 97, 1.0], ...] |
... and 4 more rows.
image_segmentation
plane_segmentations
plane_segmentation_FOV1_channel1
imaging_plane
optical_channel
0
device
table
| pixel_mask | |
|---|---|
| id | |
| 0 | [[150, 83, 1.0], [151, 83, 1.0], [152, 83, 1.0], [153, 83, 1.0], [154, 83, 1.0], [155, 83, 1.0], [156, 83, 1.0], [157, 83, 1.0], [158, 83, 1.0], [159, 83, 1.0], [160, 83, 1.0], [161, 83, 1.0], [149, 84, 1.0], [150, 84, 1.0], [151, 84, 1.0], [152, 84, 1.0], [153, 84, 1.0], [154, 84, 1.0], [155, 84, 1.0], [156, 84, 1.0], [157, 84, 1.0], [158, 84, 1.0], [159, 84, 1.0], [160, 84, 1.0], [161, 84, 1.0], [162, 84, 1.0], [163, 84, 1.0], [147, 85, 1.0], [148, 85, 1.0], [149, 85, 1.0], [150, 85, 1.0], [151, 85, 1.0], [152, 85, 1.0], [153, 85, 1.0], [154, 85, 1.0], [155, 85, 1.0], [156, 85, 1.0], [157, 85, 1.0], [158, 85, 1.0], [159, 85, 1.0], [160, 85, 1.0], [161, 85, 1.0], [162, 85, 1.0], [163, 85, 1.0], [164, 85, 1.0], [147, 86, 1.0], [148, 86, 1.0], [149, 86, 1.0], [150, 86, 1.0], [151, 86, 1.0], [152, 86, 1.0], [153, 86, 1.0], [154, 86, 1.0], [155, 86, 1.0], [156, 86, 1.0], [157, 86, 1.0], [158, 86, 1.0], [159, 86, 1.0], [160, 86, 1.0], [161, 86, 1.0], [162, 86, 1.0], [163, 86, 1.0], [164, 86, 1.0], [146, 87, 1.0], [147, 87, 1.0], [148, 87, 1.0], [149, 87, 1.0], [150, 87, 1.0], [151, 87, 1.0], [152, 87, 1.0], [153, 87, 1.0], [154, 87, 1.0], [155, 87, 1.0], [156, 87, 1.0], [157, 87, 1.0], [158, 87, 1.0], [159, 87, 1.0], [160, 87, 1.0], [161, 87, 1.0], [162, 87, 1.0], [163, 87, 1.0], [164, 87, 1.0], [147, 88, 1.0], [148, 88, 1.0], [149, 88, 1.0], [150, 88, 1.0], [151, 88, 1.0], [152, 88, 1.0], [153, 88, 1.0], [154, 88, 1.0], [155, 88, 1.0], [156, 88, 1.0], [157, 88, 1.0], [158, 88, 1.0], [159, 88, 1.0], [160, 88, 1.0], [161, 88, 1.0], [162, 88, 1.0], [163, 88, 1.0], [148, 89, 1.0], ...] |
| 1 | [[152, 91, 1.0], [153, 91, 1.0], [154, 91, 1.0], [155, 91, 1.0], [156, 91, 1.0], [150, 92, 1.0], [151, 92, 1.0], [152, 92, 1.0], [153, 92, 1.0], [154, 92, 1.0], [155, 92, 1.0], [156, 92, 1.0], [157, 92, 1.0], [149, 93, 1.0], [150, 93, 1.0], [151, 93, 1.0], [152, 93, 1.0], [153, 93, 1.0], [154, 93, 1.0], [155, 93, 1.0], [156, 93, 1.0], [157, 93, 1.0], [158, 93, 1.0], [148, 94, 1.0], [149, 94, 1.0], [150, 94, 1.0], [151, 94, 1.0], [152, 94, 1.0], [153, 94, 1.0], [154, 94, 1.0], [155, 94, 1.0], [156, 94, 1.0], [157, 94, 1.0], [158, 94, 1.0], [159, 94, 1.0], [148, 95, 1.0], [149, 95, 1.0], [150, 95, 1.0], [151, 95, 1.0], [152, 95, 1.0], [153, 95, 1.0], [154, 95, 1.0], [155, 95, 1.0], [156, 95, 1.0], [157, 95, 1.0], [158, 95, 1.0], [159, 95, 1.0], [160, 95, 1.0], [148, 96, 1.0], [149, 96, 1.0], [150, 96, 1.0], [151, 96, 1.0], [152, 96, 1.0], [153, 96, 1.0], [154, 96, 1.0], [155, 96, 1.0], [156, 96, 1.0], [157, 96, 1.0], [158, 96, 1.0], [159, 96, 1.0], [160, 96, 1.0], [147, 97, 1.0], [148, 97, 1.0], [149, 97, 1.0], [150, 97, 1.0], [151, 97, 1.0], [152, 97, 1.0], [153, 97, 1.0], [154, 97, 1.0], [155, 97, 1.0], [156, 97, 1.0], [157, 97, 1.0], [158, 97, 1.0], [159, 97, 1.0], [160, 97, 1.0], [161, 97, 1.0], [147, 98, 1.0], [148, 98, 1.0], [149, 98, 1.0], [150, 98, 1.0], [151, 98, 1.0], [152, 98, 1.0], [153, 98, 1.0], [154, 98, 1.0], [155, 98, 1.0], [156, 98, 1.0], [157, 98, 1.0], [158, 98, 1.0], [159, 98, 1.0], [160, 98, 1.0], [161, 98, 1.0], [148, 99, 1.0], [149, 99, 1.0], [150, 99, 1.0], [151, 99, 1.0], [152, 99, 1.0], [153, 99, 1.0], [154, 99, 1.0], [155, 99, 1.0], [156, 99, 1.0], ...] |
| 2 | [[145, 100, 1.0], [146, 100, 1.0], [147, 100, 1.0], [143, 101, 1.0], [144, 101, 1.0], [145, 101, 1.0], [146, 101, 1.0], [147, 101, 1.0], [148, 101, 1.0], [149, 101, 1.0], [142, 102, 1.0], [143, 102, 1.0], [144, 102, 1.0], [145, 102, 1.0], [146, 102, 1.0], [147, 102, 1.0], [148, 102, 1.0], [149, 102, 1.0], [150, 102, 1.0], [141, 103, 1.0], [142, 103, 1.0], [143, 103, 1.0], [144, 103, 1.0], [145, 103, 1.0], [146, 103, 1.0], [147, 103, 1.0], [148, 103, 1.0], [149, 103, 1.0], [150, 103, 1.0], [151, 103, 1.0], [140, 104, 1.0], [141, 104, 1.0], [142, 104, 1.0], [143, 104, 1.0], [144, 104, 1.0], [145, 104, 1.0], [146, 104, 1.0], [147, 104, 1.0], [148, 104, 1.0], [149, 104, 1.0], [150, 104, 1.0], [151, 104, 1.0], [152, 104, 1.0], [140, 105, 1.0], [141, 105, 1.0], [142, 105, 1.0], [143, 105, 1.0], [144, 105, 1.0], [145, 105, 1.0], [146, 105, 1.0], [147, 105, 1.0], [148, 105, 1.0], [149, 105, 1.0], [150, 105, 1.0], [151, 105, 1.0], [152, 105, 1.0], [139, 106, 1.0], [140, 106, 1.0], [141, 106, 1.0], [142, 106, 1.0], [143, 106, 1.0], [144, 106, 1.0], [145, 106, 1.0], [146, 106, 1.0], [147, 106, 1.0], [148, 106, 1.0], [149, 106, 1.0], [150, 106, 1.0], [151, 106, 1.0], [152, 106, 1.0], [139, 107, 1.0], [140, 107, 1.0], [141, 107, 1.0], [142, 107, 1.0], [143, 107, 1.0], [144, 107, 1.0], [145, 107, 1.0], [146, 107, 1.0], [147, 107, 1.0], [148, 107, 1.0], [149, 107, 1.0], [150, 107, 1.0], [151, 107, 1.0], [152, 107, 1.0], [139, 108, 1.0], [140, 108, 1.0], [141, 108, 1.0], [142, 108, 1.0], [143, 108, 1.0], [144, 108, 1.0], [145, 108, 1.0], [146, 108, 1.0], [147, 108, 1.0], [148, 108, 1.0], [149, 108, 1.0], [150, 108, 1.0], [151, 108, 1.0], [152, 108, 1.0], [140, 109, 1.0], [141, 109, 1.0], ...] |
| 3 | [[138, 90, 1.0], [139, 90, 1.0], [140, 90, 1.0], [137, 91, 1.0], [138, 91, 1.0], [139, 91, 1.0], [140, 91, 1.0], [141, 91, 1.0], [136, 92, 1.0], [137, 92, 1.0], [138, 92, 1.0], [139, 92, 1.0], [140, 92, 1.0], [141, 92, 1.0], [142, 92, 1.0], [143, 92, 1.0], [135, 93, 1.0], [136, 93, 1.0], [137, 93, 1.0], [138, 93, 1.0], [139, 93, 1.0], [140, 93, 1.0], [141, 93, 1.0], [142, 93, 1.0], [143, 93, 1.0], [144, 93, 1.0], [134, 94, 1.0], [135, 94, 1.0], [136, 94, 1.0], [137, 94, 1.0], [138, 94, 1.0], [139, 94, 1.0], [140, 94, 1.0], [141, 94, 1.0], [142, 94, 1.0], [143, 94, 1.0], [144, 94, 1.0], [134, 95, 1.0], [135, 95, 1.0], [136, 95, 1.0], [137, 95, 1.0], [138, 95, 1.0], [139, 95, 1.0], [140, 95, 1.0], [141, 95, 1.0], [142, 95, 1.0], [143, 95, 1.0], [144, 95, 1.0], [145, 95, 1.0], [134, 96, 1.0], [135, 96, 1.0], [136, 96, 1.0], [137, 96, 1.0], [138, 96, 1.0], [139, 96, 1.0], [140, 96, 1.0], [141, 96, 1.0], [142, 96, 1.0], [143, 96, 1.0], [144, 96, 1.0], [135, 97, 1.0], [136, 97, 1.0], [137, 97, 1.0], [138, 97, 1.0], [139, 97, 1.0], [140, 97, 1.0], [141, 97, 1.0], [142, 97, 1.0], [143, 97, 1.0], [144, 97, 1.0], [135, 98, 1.0], [136, 98, 1.0], [137, 98, 1.0], [138, 98, 1.0], [139, 98, 1.0], [140, 98, 1.0], [141, 98, 1.0], [142, 98, 1.0], [143, 98, 1.0], [144, 98, 1.0], [136, 99, 1.0], [137, 99, 1.0], [138, 99, 1.0], [139, 99, 1.0], [140, 99, 1.0], [141, 99, 1.0], [142, 99, 1.0], [143, 99, 1.0], [137, 100, 1.0], [138, 100, 1.0], [139, 100, 1.0], [140, 100, 1.0], [141, 100, 1.0], [142, 100, 1.0], [138, 101, 1.0], [139, 101, 1.0], [140, 101, 1.0]] |
... and 13 more rows.
plane_segmentation_FOV2_channel1
imaging_plane
optical_channel
0
device
table
| pixel_mask | |
|---|---|
| id | |
| 0 | [[159, 51, 1.0], [160, 51, 1.0], [154, 52, 1.0], [155, 52, 1.0], [156, 52, 1.0], [157, 52, 1.0], [158, 52, 1.0], [159, 52, 1.0], [160, 52, 1.0], [161, 52, 1.0], [162, 52, 1.0], [151, 53, 1.0], [152, 53, 1.0], [153, 53, 1.0], [154, 53, 1.0], [155, 53, 1.0], [156, 53, 1.0], [157, 53, 1.0], [158, 53, 1.0], [159, 53, 1.0], [160, 53, 1.0], [161, 53, 1.0], [162, 53, 1.0], [163, 53, 1.0], [150, 54, 1.0], [151, 54, 1.0], [152, 54, 1.0], [153, 54, 1.0], [154, 54, 1.0], [155, 54, 1.0], [156, 54, 1.0], [157, 54, 1.0], [158, 54, 1.0], [159, 54, 1.0], [160, 54, 1.0], [161, 54, 1.0], [162, 54, 1.0], [163, 54, 1.0], [149, 55, 1.0], [150, 55, 1.0], [151, 55, 1.0], [152, 55, 1.0], [153, 55, 1.0], [154, 55, 1.0], [155, 55, 1.0], [156, 55, 1.0], [157, 55, 1.0], [158, 55, 1.0], [159, 55, 1.0], [160, 55, 1.0], [161, 55, 1.0], [162, 55, 1.0], [163, 55, 1.0], [164, 55, 1.0], [149, 56, 1.0], [150, 56, 1.0], [151, 56, 1.0], [152, 56, 1.0], [153, 56, 1.0], [154, 56, 1.0], [155, 56, 1.0], [156, 56, 1.0], [157, 56, 1.0], [158, 56, 1.0], [159, 56, 1.0], [160, 56, 1.0], [161, 56, 1.0], [162, 56, 1.0], [163, 56, 1.0], [164, 56, 1.0], [148, 57, 1.0], [149, 57, 1.0], [150, 57, 1.0], [151, 57, 1.0], [152, 57, 1.0], [153, 57, 1.0], [154, 57, 1.0], [155, 57, 1.0], [156, 57, 1.0], [157, 57, 1.0], [158, 57, 1.0], [159, 57, 1.0], [160, 57, 1.0], [161, 57, 1.0], [162, 57, 1.0], [163, 57, 1.0], [164, 57, 1.0], [165, 57, 1.0], [148, 58, 1.0], [149, 58, 1.0], [150, 58, 1.0], [151, 58, 1.0], [152, 58, 1.0], [153, 58, 1.0], [154, 58, 1.0], [155, 58, 1.0], [156, 58, 1.0], [157, 58, 1.0], [158, 58, 1.0], [159, 58, 1.0], ...] |
| 1 | [[136, 63, 1.0], [137, 63, 1.0], [138, 63, 1.0], [139, 63, 1.0], [140, 63, 1.0], [141, 63, 1.0], [135, 64, 1.0], [136, 64, 1.0], [137, 64, 1.0], [138, 64, 1.0], [139, 64, 1.0], [140, 64, 1.0], [141, 64, 1.0], [142, 64, 1.0], [143, 64, 1.0], [134, 65, 1.0], [135, 65, 1.0], [136, 65, 1.0], [137, 65, 1.0], [138, 65, 1.0], [139, 65, 1.0], [140, 65, 1.0], [141, 65, 1.0], [142, 65, 1.0], [143, 65, 1.0], [133, 66, 1.0], [134, 66, 1.0], [135, 66, 1.0], [136, 66, 1.0], [137, 66, 1.0], [138, 66, 1.0], [139, 66, 1.0], [140, 66, 1.0], [141, 66, 1.0], [142, 66, 1.0], [143, 66, 1.0], [144, 66, 1.0], [133, 67, 1.0], [134, 67, 1.0], [135, 67, 1.0], [136, 67, 1.0], [137, 67, 1.0], [138, 67, 1.0], [139, 67, 1.0], [140, 67, 1.0], [141, 67, 1.0], [142, 67, 1.0], [143, 67, 1.0], [144, 67, 1.0], [145, 67, 1.0], [133, 68, 1.0], [134, 68, 1.0], [135, 68, 1.0], [136, 68, 1.0], [137, 68, 1.0], [138, 68, 1.0], [139, 68, 1.0], [140, 68, 1.0], [141, 68, 1.0], [142, 68, 1.0], [143, 68, 1.0], [144, 68, 1.0], [145, 68, 1.0], [132, 69, 1.0], [133, 69, 1.0], [134, 69, 1.0], [135, 69, 1.0], [136, 69, 1.0], [137, 69, 1.0], [138, 69, 1.0], [139, 69, 1.0], [140, 69, 1.0], [141, 69, 1.0], [142, 69, 1.0], [143, 69, 1.0], [144, 69, 1.0], [145, 69, 1.0], [146, 69, 1.0], [132, 70, 1.0], [133, 70, 1.0], [134, 70, 1.0], [135, 70, 1.0], [136, 70, 1.0], [137, 70, 1.0], [138, 70, 1.0], [139, 70, 1.0], [140, 70, 1.0], [141, 70, 1.0], [142, 70, 1.0], [143, 70, 1.0], [144, 70, 1.0], [145, 70, 1.0], [146, 70, 1.0], [147, 70, 1.0], [132, 71, 1.0], [133, 71, 1.0], [134, 71, 1.0], [135, 71, 1.0], [136, 71, 1.0], [137, 71, 1.0], ...] |
| 2 | [[144, 96, 1.0], [145, 96, 1.0], [150, 96, 1.0], [151, 96, 1.0], [142, 97, 1.0], [143, 97, 1.0], [144, 97, 1.0], [145, 97, 1.0], [146, 97, 1.0], [147, 97, 1.0], [148, 97, 1.0], [149, 97, 1.0], [150, 97, 1.0], [151, 97, 1.0], [152, 97, 1.0], [140, 98, 1.0], [141, 98, 1.0], [142, 98, 1.0], [143, 98, 1.0], [144, 98, 1.0], [145, 98, 1.0], [146, 98, 1.0], [147, 98, 1.0], [148, 98, 1.0], [149, 98, 1.0], [150, 98, 1.0], [151, 98, 1.0], [152, 98, 1.0], [153, 98, 1.0], [139, 99, 1.0], [140, 99, 1.0], [141, 99, 1.0], [142, 99, 1.0], [143, 99, 1.0], [144, 99, 1.0], [145, 99, 1.0], [146, 99, 1.0], [147, 99, 1.0], [148, 99, 1.0], [149, 99, 1.0], [150, 99, 1.0], [151, 99, 1.0], [152, 99, 1.0], [153, 99, 1.0], [139, 100, 1.0], [140, 100, 1.0], [141, 100, 1.0], [142, 100, 1.0], [143, 100, 1.0], [144, 100, 1.0], [145, 100, 1.0], [146, 100, 1.0], [147, 100, 1.0], [148, 100, 1.0], [149, 100, 1.0], [150, 100, 1.0], [151, 100, 1.0], [152, 100, 1.0], [153, 100, 1.0], [139, 101, 1.0], [140, 101, 1.0], [141, 101, 1.0], [142, 101, 1.0], [143, 101, 1.0], [144, 101, 1.0], [145, 101, 1.0], [146, 101, 1.0], [147, 101, 1.0], [148, 101, 1.0], [149, 101, 1.0], [150, 101, 1.0], [151, 101, 1.0], [152, 101, 1.0], [153, 101, 1.0], [140, 102, 1.0], [141, 102, 1.0], [142, 102, 1.0], [143, 102, 1.0], [144, 102, 1.0], [145, 102, 1.0], [146, 102, 1.0], [147, 102, 1.0], [148, 102, 1.0], [149, 102, 1.0], [150, 102, 1.0], [151, 102, 1.0], [152, 102, 1.0], [142, 103, 1.0], [143, 103, 1.0], [144, 103, 1.0], [145, 103, 1.0], [146, 103, 1.0], [147, 103, 1.0], [148, 103, 1.0], [149, 103, 1.0], [150, 103, 1.0], [151, 103, 1.0], [143, 104, 1.0], [144, 104, 1.0], [145, 104, 1.0], ...] |
| 3 | [[146, 85, 1.0], [144, 86, 1.0], [145, 86, 1.0], [146, 86, 1.0], [147, 86, 1.0], [148, 86, 1.0], [149, 86, 1.0], [143, 87, 1.0], [144, 87, 1.0], [145, 87, 1.0], [146, 87, 1.0], [147, 87, 1.0], [148, 87, 1.0], [149, 87, 1.0], [150, 87, 1.0], [142, 88, 1.0], [143, 88, 1.0], [144, 88, 1.0], [145, 88, 1.0], [146, 88, 1.0], [147, 88, 1.0], [148, 88, 1.0], [149, 88, 1.0], [150, 88, 1.0], [142, 89, 1.0], [143, 89, 1.0], [144, 89, 1.0], [145, 89, 1.0], [146, 89, 1.0], [147, 89, 1.0], [148, 89, 1.0], [149, 89, 1.0], [150, 89, 1.0], [151, 89, 1.0], [141, 90, 1.0], [142, 90, 1.0], [143, 90, 1.0], [144, 90, 1.0], [145, 90, 1.0], [146, 90, 1.0], [147, 90, 1.0], [148, 90, 1.0], [149, 90, 1.0], [150, 90, 1.0], [151, 90, 1.0], [152, 90, 1.0], [141, 91, 1.0], [142, 91, 1.0], [143, 91, 1.0], [144, 91, 1.0], [145, 91, 1.0], [146, 91, 1.0], [147, 91, 1.0], [148, 91, 1.0], [149, 91, 1.0], [150, 91, 1.0], [151, 91, 1.0], [152, 91, 1.0], [142, 92, 1.0], [143, 92, 1.0], [144, 92, 1.0], [145, 92, 1.0], [146, 92, 1.0], [147, 92, 1.0], [148, 92, 1.0], [149, 92, 1.0], [150, 92, 1.0], [151, 92, 1.0], [152, 92, 1.0], [142, 93, 1.0], [143, 93, 1.0], [144, 93, 1.0], [145, 93, 1.0], [146, 93, 1.0], [147, 93, 1.0], [148, 93, 1.0], [149, 93, 1.0], [150, 93, 1.0], [151, 93, 1.0], [152, 93, 1.0], [143, 94, 1.0], [144, 94, 1.0], [145, 94, 1.0], [146, 94, 1.0], [147, 94, 1.0], [148, 94, 1.0], [149, 94, 1.0], [150, 94, 1.0], [151, 94, 1.0], [144, 95, 1.0], [145, 95, 1.0], [146, 95, 1.0], [147, 95, 1.0], [148, 95, 1.0], [149, 95, 1.0], [150, 95, 1.0], [151, 95, 1.0], [146, 96, 1.0], [147, 96, 1.0], [148, 96, 1.0], ...] |
... and 44 more rows.
plane_segmentation_FOV3_channel1
imaging_plane
optical_channel
0
device
table
| pixel_mask | |
|---|---|
| id | |
| 0 | [[335, 89, 1.0], [332, 90, 1.0], [333, 90, 1.0], [334, 90, 1.0], [335, 90, 1.0], [336, 90, 1.0], [337, 90, 1.0], [338, 90, 1.0], [339, 90, 1.0], [327, 91, 1.0], [328, 91, 1.0], [329, 91, 1.0], [330, 91, 1.0], [331, 91, 1.0], [332, 91, 1.0], [333, 91, 1.0], [334, 91, 1.0], [335, 91, 1.0], [336, 91, 1.0], [337, 91, 1.0], [338, 91, 1.0], [339, 91, 1.0], [340, 91, 1.0], [326, 92, 1.0], [327, 92, 1.0], [328, 92, 1.0], [329, 92, 1.0], [330, 92, 1.0], [331, 92, 1.0], [332, 92, 1.0], [333, 92, 1.0], [334, 92, 1.0], [335, 92, 1.0], [336, 92, 1.0], [337, 92, 1.0], [338, 92, 1.0], [339, 92, 1.0], [340, 92, 1.0], [341, 92, 1.0], [324, 93, 1.0], [325, 93, 1.0], [326, 93, 1.0], [327, 93, 1.0], [328, 93, 1.0], [329, 93, 1.0], [330, 93, 1.0], [331, 93, 1.0], [332, 93, 1.0], [333, 93, 1.0], [334, 93, 1.0], [335, 93, 1.0], [336, 93, 1.0], [337, 93, 1.0], [338, 93, 1.0], [339, 93, 1.0], [340, 93, 1.0], [341, 93, 1.0], [342, 93, 1.0], [323, 94, 1.0], [324, 94, 1.0], [325, 94, 1.0], [326, 94, 1.0], [327, 94, 1.0], [328, 94, 1.0], [329, 94, 1.0], [330, 94, 1.0], [331, 94, 1.0], [332, 94, 1.0], [333, 94, 1.0], [334, 94, 1.0], [335, 94, 1.0], [336, 94, 1.0], [337, 94, 1.0], [338, 94, 1.0], [339, 94, 1.0], [340, 94, 1.0], [341, 94, 1.0], [342, 94, 1.0], [322, 95, 1.0], [323, 95, 1.0], [324, 95, 1.0], [325, 95, 1.0], [326, 95, 1.0], [327, 95, 1.0], [328, 95, 1.0], [329, 95, 1.0], [330, 95, 1.0], [331, 95, 1.0], [332, 95, 1.0], [333, 95, 1.0], [334, 95, 1.0], [335, 95, 1.0], [336, 95, 1.0], [337, 95, 1.0], [338, 95, 1.0], [339, 95, 1.0], [340, 95, 1.0], [341, 95, 1.0], [342, 95, 1.0], [343, 95, 1.0], ...] |
| 1 | [[325, 77, 1.0], [326, 77, 1.0], [327, 77, 1.0], [328, 77, 1.0], [329, 77, 1.0], [323, 78, 1.0], [324, 78, 1.0], [325, 78, 1.0], [326, 78, 1.0], [327, 78, 1.0], [328, 78, 1.0], [329, 78, 1.0], [330, 78, 1.0], [321, 79, 1.0], [322, 79, 1.0], [323, 79, 1.0], [324, 79, 1.0], [325, 79, 1.0], [326, 79, 1.0], [327, 79, 1.0], [328, 79, 1.0], [329, 79, 1.0], [330, 79, 1.0], [331, 79, 1.0], [320, 80, 1.0], [321, 80, 1.0], [322, 80, 1.0], [323, 80, 1.0], [324, 80, 1.0], [325, 80, 1.0], [326, 80, 1.0], [327, 80, 1.0], [328, 80, 1.0], [329, 80, 1.0], [330, 80, 1.0], [331, 80, 1.0], [332, 80, 1.0], [319, 81, 1.0], [320, 81, 1.0], [321, 81, 1.0], [322, 81, 1.0], [323, 81, 1.0], [324, 81, 1.0], [325, 81, 1.0], [326, 81, 1.0], [327, 81, 1.0], [328, 81, 1.0], [329, 81, 1.0], [330, 81, 1.0], [331, 81, 1.0], [332, 81, 1.0], [319, 82, 1.0], [320, 82, 1.0], [321, 82, 1.0], [322, 82, 1.0], [323, 82, 1.0], [324, 82, 1.0], [325, 82, 1.0], [326, 82, 1.0], [327, 82, 1.0], [328, 82, 1.0], [329, 82, 1.0], [330, 82, 1.0], [331, 82, 1.0], [332, 82, 1.0], [333, 82, 1.0], [318, 83, 1.0], [319, 83, 1.0], [320, 83, 1.0], [321, 83, 1.0], [322, 83, 1.0], [323, 83, 1.0], [324, 83, 1.0], [325, 83, 1.0], [326, 83, 1.0], [327, 83, 1.0], [328, 83, 1.0], [329, 83, 1.0], [330, 83, 1.0], [331, 83, 1.0], [332, 83, 1.0], [333, 83, 1.0], [334, 83, 1.0], [318, 84, 1.0], [319, 84, 1.0], [320, 84, 1.0], [321, 84, 1.0], [322, 84, 1.0], [323, 84, 1.0], [324, 84, 1.0], [325, 84, 1.0], [326, 84, 1.0], [327, 84, 1.0], [328, 84, 1.0], [329, 84, 1.0], [330, 84, 1.0], [331, 84, 1.0], [332, 84, 1.0], [333, 84, 1.0], [334, 84, 1.0], ...] |
| 2 | [[351, 92, 1.0], [352, 92, 1.0], [353, 92, 1.0], [354, 92, 1.0], [355, 92, 1.0], [349, 93, 1.0], [350, 93, 1.0], [351, 93, 1.0], [352, 93, 1.0], [353, 93, 1.0], [354, 93, 1.0], [355, 93, 1.0], [356, 93, 1.0], [357, 93, 1.0], [347, 94, 1.0], [348, 94, 1.0], [349, 94, 1.0], [350, 94, 1.0], [351, 94, 1.0], [352, 94, 1.0], [353, 94, 1.0], [354, 94, 1.0], [355, 94, 1.0], [356, 94, 1.0], [357, 94, 1.0], [358, 94, 1.0], [347, 95, 1.0], [348, 95, 1.0], [349, 95, 1.0], [350, 95, 1.0], [351, 95, 1.0], [352, 95, 1.0], [353, 95, 1.0], [354, 95, 1.0], [355, 95, 1.0], [356, 95, 1.0], [357, 95, 1.0], [358, 95, 1.0], [359, 95, 1.0], [346, 96, 1.0], [347, 96, 1.0], [348, 96, 1.0], [349, 96, 1.0], [350, 96, 1.0], [351, 96, 1.0], [352, 96, 1.0], [353, 96, 1.0], [354, 96, 1.0], [355, 96, 1.0], [356, 96, 1.0], [357, 96, 1.0], [358, 96, 1.0], [359, 96, 1.0], [360, 96, 1.0], [345, 97, 1.0], [346, 97, 1.0], [347, 97, 1.0], [348, 97, 1.0], [349, 97, 1.0], [350, 97, 1.0], [351, 97, 1.0], [352, 97, 1.0], [353, 97, 1.0], [354, 97, 1.0], [355, 97, 1.0], [356, 97, 1.0], [357, 97, 1.0], [358, 97, 1.0], [359, 97, 1.0], [360, 97, 1.0], [361, 97, 1.0], [344, 98, 1.0], [345, 98, 1.0], [346, 98, 1.0], [347, 98, 1.0], [348, 98, 1.0], [349, 98, 1.0], [350, 98, 1.0], [351, 98, 1.0], [352, 98, 1.0], [353, 98, 1.0], [354, 98, 1.0], [355, 98, 1.0], [356, 98, 1.0], [357, 98, 1.0], [358, 98, 1.0], [359, 98, 1.0], [360, 98, 1.0], [361, 98, 1.0], [362, 98, 1.0], [344, 99, 1.0], [345, 99, 1.0], [346, 99, 1.0], [347, 99, 1.0], [348, 99, 1.0], [349, 99, 1.0], [350, 99, 1.0], [351, 99, 1.0], [352, 99, 1.0], [353, 99, 1.0], ...] |
| 3 | [[296, 90, 1.0], [297, 90, 1.0], [293, 91, 1.0], [294, 91, 1.0], [295, 91, 1.0], [296, 91, 1.0], [297, 91, 1.0], [298, 91, 1.0], [299, 91, 1.0], [300, 91, 1.0], [291, 92, 1.0], [292, 92, 1.0], [293, 92, 1.0], [294, 92, 1.0], [295, 92, 1.0], [296, 92, 1.0], [297, 92, 1.0], [298, 92, 1.0], [299, 92, 1.0], [300, 92, 1.0], [301, 92, 1.0], [289, 93, 1.0], [290, 93, 1.0], [291, 93, 1.0], [292, 93, 1.0], [293, 93, 1.0], [294, 93, 1.0], [295, 93, 1.0], [296, 93, 1.0], [297, 93, 1.0], [298, 93, 1.0], [299, 93, 1.0], [300, 93, 1.0], [301, 93, 1.0], [302, 93, 1.0], [288, 94, 1.0], [289, 94, 1.0], [290, 94, 1.0], [291, 94, 1.0], [292, 94, 1.0], [293, 94, 1.0], [294, 94, 1.0], [295, 94, 1.0], [296, 94, 1.0], [297, 94, 1.0], [298, 94, 1.0], [299, 94, 1.0], [300, 94, 1.0], [301, 94, 1.0], [302, 94, 1.0], [287, 95, 1.0], [288, 95, 1.0], [289, 95, 1.0], [290, 95, 1.0], [291, 95, 1.0], [292, 95, 1.0], [293, 95, 1.0], [294, 95, 1.0], [295, 95, 1.0], [296, 95, 1.0], [297, 95, 1.0], [298, 95, 1.0], [299, 95, 1.0], [300, 95, 1.0], [301, 95, 1.0], [302, 95, 1.0], [303, 95, 1.0], [286, 96, 1.0], [287, 96, 1.0], [288, 96, 1.0], [289, 96, 1.0], [290, 96, 1.0], [291, 96, 1.0], [292, 96, 1.0], [293, 96, 1.0], [294, 96, 1.0], [295, 96, 1.0], [296, 96, 1.0], [297, 96, 1.0], [298, 96, 1.0], [299, 96, 1.0], [300, 96, 1.0], [301, 96, 1.0], [302, 96, 1.0], [303, 96, 1.0], [286, 97, 1.0], [287, 97, 1.0], [288, 97, 1.0], [289, 97, 1.0], [290, 97, 1.0], [291, 97, 1.0], [292, 97, 1.0], [293, 97, 1.0], [294, 97, 1.0], [295, 97, 1.0], [296, 97, 1.0], [297, 97, 1.0], [298, 97, 1.0], [299, 97, 1.0], [300, 97, 1.0], ...] |
... and 4 more rows.
Plot Correlation Images¶
correlation_images_names = list(nwbfile.processing["ophys"]["correlation_images"].images.keys())
_ = [print(name) for name in correlation_images_names]
correlation_image_FOV1_channel1 correlation_image_FOV2_channel1 correlation_image_FOV3_channel1
fig, axs = plt.subplots(nrows=len(correlation_images_names), ncols=1, sharex=True, sharey=True)
for ci_index,ci_name in enumerate(correlation_images_names):
correlation_image = nwbfile.processing["ophys"]["correlation_images"].images[ci_name]
axs[ci_index].imshow(correlation_image.data[:].T, cmap="binary")
axs[ci_index].set_title(ci_name.replace("_"," "))
plt.show()
Plot Average Images¶
average_images_names = list(nwbfile.processing["ophys"]["average_images"].images.keys())
_ = [print(name) for name in average_images_names]
average_image_FOV1_channel1 average_image_FOV2_channel1 average_image_FOV3_channel1
fig, axs = plt.subplots(nrows=len(average_images_names), ncols=1, sharex=True, sharey=True)
for ai_index,ai_name in enumerate(average_images_names):
average_image = nwbfile.processing["ophys"]["average_images"].images[ai_name]
axs[ai_index].imshow(average_image.data[:].T, cmap="binary")
axs[ai_index].set_title(ai_name.replace("_"," "))
plt.show()
Plot Image Segmentation¶
plane_segmentation_names = list(nwbfile.processing["ophys"]["image_segmentation"].plane_segmentations.keys())
_ = [print(name) for name in nwbfile.processing["ophys"]["image_segmentation"].plane_segmentations.keys()]
plane_segmentation_FOV1_channel1 plane_segmentation_FOV2_channel1 plane_segmentation_FOV3_channel1
ROI_index = 0
fig, axs = plt.subplots(nrows=len(plane_segmentation_names), ncols=1, sharex=True, sharey=True)
for ps_index,ps_name in enumerate(plane_segmentation_names):
average_image = nwbfile.processing["ophys"]["average_images"].images[average_images_names[ps_index]]
axs[ps_index].imshow(average_image.data[:].T, cmap="binary")
plane_segmentation = nwbfile.processing["ophys"]["image_segmentation"].plane_segmentations[ps_name]
x_coordinates = [pix[0] for pix in plane_segmentation[ROI_index].pixel_mask[0]]
y_coordinates = [pix[1] for pix in plane_segmentation[ROI_index].pixel_mask[0]]
axs[ps_index].scatter(x_coordinates, y_coordinates, color="green")
axs[ps_index].set_title(ps_name.replace("_"," "))
plt.show()
Visualize fluorescence traces¶
The fluroscence traces are stored in a Fluorescence container, the raw traces can be accessed as nwbfile.processing["ophys"]["Fluorescence"]["RoiResponseSeries"].
import pandas as pd
import warnings
warnings.simplefilter(action='ignore', category=pd.errors.PerformanceWarning)
fluorescence_traces_names = [name for name in nwbfile.processing["ophys"]["fluorescence"].roi_response_series.keys()]
fluorescence_traces_name = fluorescence_traces_names[0]
fluorescence_traces = nwbfile.processing["ophys"]["fluorescence"][fluorescence_traces_name].data[:1000, :10]
df = pd.DataFrame(fluorescence_traces)
df["time"] = nwbfile.processing["ophys"]["fluorescence"][fluorescence_traces_name].timestamps[:1000]
df.set_index("time", inplace=True)
df.columns.name = 'ROIs'
import plotly.express as px
fig = px.line(df, facet_row="ROIs", facet_row_spacing=0.01)
# hide and lock down axes
fig.update_xaxes(visible=True, fixedrange=False)
fig.update_yaxes(visible=False, fixedrange=False)
# remove facet/subplot labels
fig.update_layout(annotations=[], overwrite=True)
# strip down the rest of the plot
fig.update_layout(
showlegend=True,
plot_bgcolor="white",
margin=dict(t=10, l=10, b=10, r=10)
)
fig.show(config=dict(displayModeBar=True))
Access Odor stimuli ¶
This section demonstrates how to access the odor stimulation data and metadata.
nwbfile.trials.to_dataframe()
| start_time | stop_time | odorant | concentration | solution_date | |
|---|---|---|---|---|---|
| id | |||||
| 0 | 59.2888 | 60.2928 | Methyl Salicylate | 0.1 | 2022-05-17 |
| 1 | 60.2966 | 61.2995 | Methyl Salicylate | 0.1 | 2022-05-17 |
| 2 | 61.3034 | 62.3067 | Methyl Salicylate | 0.1 | 2022-05-17 |
| 3 | 62.3106 | 63.3130 | Methyl Salicylate | 0.1 | 2022-05-17 |
| 4 | 63.3170 | 64.3213 | Methyl Salicylate | 0.1 | 2022-05-17 |
| ... | ... | ... | ... | ... | ... |
| 495 | 9675.0000 | 9676.0000 | Methyl Salicylate | 0.1 | 2022-05-17 |
| 496 | 9676.0000 | 9677.0100 | Methyl Salicylate | 0.1 | 2022-05-17 |
| 497 | 9677.0100 | 9678.0100 | Methyl Salicylate | 0.1 | 2022-05-17 |
| 498 | 9678.0200 | 9679.0200 | Methyl Salicylate | 0.1 | 2022-05-17 |
| 499 | 9679.0200 | 9680.0300 | Methyl Salicylate | 0.1 | 2022-05-17 |
500 rows × 5 columns
# Prepare data for plotting
import numpy as np
ROI_index=0
start=0
stop=-1
fluorescence_data = nwbfile.processing["ophys"]["fluorescence"][fluorescence_traces_name].data[start:stop, ROI_index]
fluorescence_timestamps = nwbfile.processing["ophys"]["fluorescence"][fluorescence_traces_name].timestamps[start:stop]
fig, ax = plt.subplots(figsize=(6, 2), dpi=300)
line_handle, = ax.plot(fluorescence_timestamps, fluorescence_data, color="green", linewidth=0.5, label="ROI {ROI_index}".format(ROI_index=ROI_index))
stimulus_table = nwbfile.trials.to_dataframe()
methyl_salicylate_stim = "Methyl Salicylate"
methyl_salicylate_stim_table = stimulus_table[stimulus_table["odorant"]==methyl_salicylate_stim]
methyl_salicylate_stim_handles = []
for (stimulus_start, stimulus_stop) in zip(methyl_salicylate_stim_table["start_time"], methyl_salicylate_stim_table["stop_time"]):
methyl_salicylate_stim_handle = ax.fill_between(fluorescence_timestamps, np.nanmax(fluorescence_data), where=(fluorescence_timestamps >= stimulus_start) & (fluorescence_timestamps <= stimulus_stop),
color='yellow', edgecolor='none', alpha=0.9, label=methyl_salicylate_stim)
methyl_salicylate_stim_handles.append(methyl_salicylate_stim_handle)
allyl_sulfide_stim = "Allyl Sulfide"
allyl_sulfide_stim_table = stimulus_table[stimulus_table["odorant"]==allyl_sulfide_stim]
allyl_sulfide_stim_handles = []
for (stimulus_start, stimulus_stop) in zip(allyl_sulfide_stim_table["start_time"], allyl_sulfide_stim_table["stop_time"]):
allyl_sulfide_stim_handle = ax.fill_between(fluorescence_timestamps, np.nanmax(fluorescence_data), where=(fluorescence_timestamps >= stimulus_start) & (fluorescence_timestamps <= stimulus_stop),
color='blue', edgecolor='none', alpha=0.9, label=allyl_sulfide_stim)
allyl_sulfide_stim_handles.append(allyl_sulfide_stim_handle)
# Hide top and right spines
ax.spines['top'].set_visible(False)
ax.spines['right'].set_visible(False)
# Create the legend with the appropriate handles
handles = [line_handle, methyl_salicylate_stim_handles[0], allyl_sulfide_stim_handles[0]]
labels = ["ROI {ROI_index}".format(ROI_index=ROI_index), methyl_salicylate_stim, allyl_sulfide_stim]
ax.legend(handles, labels, frameon=False, bbox_to_anchor=(.95, 1), loc='upper left', prop={'size': 8})
ax.tick_params(axis='y', labelsize=8)
plt.xlabel('Time (s)', fontsize=8)
plt.tick_params(axis='x', labelsize=8)
plt.show()
Access Treadmill Traces ¶
This section demonstrates how to access the treadmill data.
nwbfile.acquisition["treadmill_position"]
treadmill_position (SpatialSeries)
data
timestamps
timestamp_link
start=0
stop=-1
treadmill_data = nwbfile.acquisition["treadmill_position"].data[start:stop]
treadmill_timestamps = nwbfile.acquisition["treadmill_position"].timestamps[start:stop]
fig, ax = plt.subplots(figsize=(6, 2), dpi=300)
ax.plot(treadmill_timestamps, treadmill_data, color="red", linewidth=0.5, label="treadmill position")
# Hide top and right spines
ax.spines['top'].set_visible(False)
ax.spines['right'].set_visible(False)
# Create the
ax.legend(frameon=False, bbox_to_anchor=(.95, 1), loc='upper left', prop={'size': 8})
ax.tick_params(axis='y', labelsize=8)
plt.xlabel('Time (s)', fontsize=8)
plt.tick_params(axis='x', labelsize=8)
plt.show()
nwbfile.processing["behavior"]["treadmill_velocity"]
treadmill_velocity (TimeSeries)
data
timestamps (link to acquisition/treadmill_position/timestamps)
data = nwbfile.processing["behavior"]["treadmill_velocity"].data[start:stop]
treadmill_timestamps = nwbfile.acquisition["treadmill_position"].timestamps[start:stop]
fig, ax = plt.subplots(figsize=(6, 2), dpi=300)
ax.plot(fluorescence_timestamps, fluorescence_data, linewidth=0.5, label="fluorescence trace")
ax.plot(treadmill_timestamps, data*25, linewidth=0.5, label="treadmill velocity")
# Hide top and right spines
ax.spines['top'].set_visible(False)
ax.spines['right'].set_visible(False)
# Create the
ax.legend(frameon=False, bbox_to_anchor=(.95, 1), loc='upper left', prop={'size': 8})
ax.tick_params(axis='y', labelsize=8)
plt.xlabel('Time (s)', fontsize=8)
plt.tick_params(axis='x', labelsize=8)
plt.show()